Raul Alcantara | 1 Apr 15:38 2010
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Added a finite difference check script for FFML terms

Commit from rulix 2010-04-01 15:38 CEST
Added a finite difference check script for FFML terms Module File name Revision
+ Adun Scripts/ffmlFD.st 1.1


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from rulix</td>
        <td align="right">2010-04-01 15:38 CEST</td>
      </tr></table>Added a finite difference check script for FFML terms

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemA0">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Scripts/ffmlFD.st</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/ffmlFD.st?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
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Michael Johnston | 1 Apr 18:45 2010
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Gets a requested frame and the original conf and outputs them [...]

Commit from mjohnston 2010-04-01 18:45 CEST
Gets a requested frame and the original conf and outputs them Gets a requested frame and the original conf and outputs them Module File name Revision
+ Adun Scripts/GetFrameDiff.st 1.1


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    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2010-04-01 18:45 CEST</td>
      </tr></table>Gets a requested frame and the original conf and outputs them
Gets a requested frame and the original conf and outputs them

    <table cellspacing="0" cellpadding="3" class="history">
<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemA0">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Scripts/GetFrameDiff.st</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/GetFrameDiff.st?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
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Michael Johnston | 1 Apr 18:47 2010
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Update name

Commit from mjohnston 2010-04-01 18:47 CEST
Update name Module File name Revision
- Adun Scripts/GetFrameDiff.st 1.1
+ Adun Scripts/GetFrames.st 1.1


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    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from mjohnston</td>
        <td align="right">2010-04-01 18:47 CEST</td>
      </tr></table>Update name

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemR0">
<td class="itemact">-</td>
        <td class="item">Adun</td>
        <td class="item">Scripts/GetFrameDiff.st</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/Attic/GetFrameDiff.st?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
      </tr>
<tr class="itemA1">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Scripts/GetFrames.st</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/GetFrames.st?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
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Nils Drechsel | 10 Apr 18:05 2010
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added functionality to directly read files in the CMD AMBER directory, which makes it now very easy to convert AMBER forcefields to FFML. Also added functionality to parse AMBER .lib files

Commit from nilsdrechsel 2010-04-10 18:05 CEST
added functionality to directly read files in the CMD AMBER directory, which makes it now very easy to convert AMBER forcefields to FFML. Also added functionality to parse AMBER .lib files Module File name Revision
+ Adun Scripts/parseAmberCMD.py 1.1
Adun Scripts/convert_amber_topology_to_ffml.st 1.2 >>> 1.3
Adun Scripts/convert_amber_parm_to_ffml.st 1.2 >>> 1.3


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from nilsdrechsel</td>
        <td align="right">2010-04-10 18:05 CEST</td>
      </tr></table>added functionality to directly read files in the CMD AMBER directory, which makes it now very easy to convert AMBER forcefields to FFML. Also added functionality to parse AMBER .lib files

    <table cellspacing="0" cellpadding="3" class="history">
<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemA0">
<td class="itemact">+</td>
        <td class="item">Adun</td>
        <td class="item">Scripts/parseAmberCMD.py</td>
        <td class="itemrev"></td>
        <td class="itemrev"></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/parseAmberCMD.py?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
      </tr>
<tr class="itemM1">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Scripts/convert_amber_topology_to_ffml.st</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/convert_amber_topology_to_ffml.st?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/convert_amber_topology_to_ffml.st?r1=1.2&amp;r2=1.3">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/convert_amber_topology_to_ffml.st?rev=1.3&amp;content-type=text/vnd.viewcvs-markup">1.3</a></td>
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Scripts/convert_amber_parm_to_ffml.st</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/convert_amber_parm_to_ffml.st?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/convert_amber_parm_to_ffml.st?r1=1.2&amp;r2=1.3">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/convert_amber_parm_to_ffml.st?rev=1.3&amp;content-type=text/vnd.viewcvs-markup">1.3</a></td>
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Nils Drechsel | 12 Apr 15:01 2010
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more complete version + addition of aminoacid analogues

Commit from nilsdrechsel 2010-04-12 15:01 CEST
more complete version + addition of aminoacid analogues Module File name Revision
Adun UL/ULFramework/Resources/ForceFields/Amber96/Amber96Topology.ffml 1.2 >>> 1.3


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from nilsdrechsel</td>
        <td align="right">2010-04-12 15:01 CEST</td>
      </tr></table>more complete version + addition of aminoacid analogues

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">UL/ULFramework/Resources/ForceFields/Amber96/Amber96Topology.ffml</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/ForceFields/Amber96/Amber96Topology.ffml?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/ForceFields/Amber96/Amber96Topology.ffml?r1=1.2&amp;r2=1.3">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/ForceFields/Amber96/Amber96Topology.ffml?rev=1.3&amp;content-type=text/vnd.viewcvs-markup">1.3</a></td>
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Nils Drechsel | 12 Apr 15:02 2010
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fixed an error with residue indexes

Commit from nilsdrechsel 2010-04-12 15:02 CEST
fixed an error with residue indexes Module File name Revision
Adun Scripts/convert_amber_topology_to_ffml.st 1.3 >>> 1.4


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from nilsdrechsel</td>
        <td align="right">2010-04-12 15:02 CEST</td>
      </tr></table>fixed an error with residue indexes

    <table cellspacing="0" cellpadding="3" class="history">
<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Scripts/convert_amber_topology_to_ffml.st</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/convert_amber_topology_to_ffml.st?rev=1.3&amp;content-type=text/vnd.viewcvs-markup">1.3</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/convert_amber_topology_to_ffml.st?r1=1.3&amp;r2=1.4">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Scripts/convert_amber_topology_to_ffml.st?rev=1.4&amp;content-type=text/vnd.viewcvs-markup">1.4</a></td>
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Nils Drechsel | 12 Apr 15:37 2010
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changed the identifiers of some of the aminoacid analogues

Commit from nilsdrechsel 2010-04-12 15:36 CEST
changed the identifiers of some of the aminoacid analogues Module File name Revision
Adun UL/ULFramework/Resources/ForceFields/Amber96/Amber96Topology.ffml 1.3 >>> 1.4


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from nilsdrechsel</td>
        <td align="right">2010-04-12 15:36 CEST</td>
      </tr></table>changed the identifiers of some of the aminoacid analogues

    <table cellspacing="0" cellpadding="3" class="history">
<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">UL/ULFramework/Resources/ForceFields/Amber96/Amber96Topology.ffml</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/ForceFields/Amber96/Amber96Topology.ffml?rev=1.3&amp;content-type=text/vnd.viewcvs-markup">1.3</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/ForceFields/Amber96/Amber96Topology.ffml?r1=1.3&amp;r2=1.4">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/UL/ULFramework/Resources/ForceFields/Amber96/Amber96Topology.ffml?rev=1.4&amp;content-type=text/vnd.viewcvs-markup">1.4</a></td>
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Nils Drechsel | 12 Apr 16:03 2010
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deleted nonbondedterm and forcefield dependencies

Commit from nilsdrechsel 2010-04-12 16:03 CEST
deleted nonbondedterm and forcefield dependencies Module File name Revision
Adun Kernel/AdunKernel/Headers/AdunKernel/AdunSemiExplicitSolvation.h 1.1 >>> 1.2


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from nilsdrechsel</td>
        <td align="right">2010-04-12 16:03 CEST</td>
      </tr></table>deleted nonbondedterm and forcefield dependencies

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Headers/AdunKernel/AdunSemiExplicitSolvation.h</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunSemiExplicitSolvation.h?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunSemiExplicitSolvation.h?r1=1.1&amp;r2=1.2">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Headers/AdunKernel/AdunSemiExplicitSolvation.h?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
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Nils Drechsel | 12 Apr 16:04 2010
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deleted nonbondedterm and forcefield dependencies

Commit from nilsdrechsel 2010-04-12 16:04 CEST
deleted nonbondedterm and forcefield dependencies Module File name Revision
Adun Kernel/AdunKernel/Framework/AdunSemiExplicitSolvation.mm 1.1 >>> 1.2


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from nilsdrechsel</td>
        <td align="right">2010-04-12 16:04 CEST</td>
      </tr></table>deleted nonbondedterm and forcefield dependencies

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Framework/AdunSemiExplicitSolvation.mm</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunSemiExplicitSolvation.mm?rev=1.1&amp;content-type=text/vnd.viewcvs-markup">1.1</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunSemiExplicitSolvation.mm?r1=1.1&amp;r2=1.2">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunSemiExplicitSolvation.mm?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
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Nils Drechsel | 12 Apr 16:07 2010
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forgot a dependency

Commit from nilsdrechsel 2010-04-12 16:07 CEST
forgot a dependency Module File name Revision
Adun Kernel/AdunKernel/Framework/AdunSemiExplicitSolvation.mm 1.2 >>> 1.3


<div>

    <table width="100%" class="csetheader"><tr>
<td align="left">Commit from nilsdrechsel</td>
        <td align="right">2010-04-12 16:07 CEST</td>
      </tr></table>forgot a dependency

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<tr class="history">
        Module
        File name
        Revision
      </tr>
<tr class="itemM0">
<td class="itemact"></td>
        <td class="item">Adun</td>
        <td class="item">Kernel/AdunKernel/Framework/AdunSemiExplicitSolvation.mm</td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunSemiExplicitSolvation.mm?rev=1.2&amp;content-type=text/vnd.viewcvs-markup">1.2</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunSemiExplicitSolvation.mm?r1=1.2&amp;r2=1.3">&gt;&gt;&gt;</a></td>
        <td class="itemrev"><a href="http://cvs.gna.org/viewcvs/adun/Adun/Kernel/AdunKernel/Framework/AdunSemiExplicitSolvation.mm?rev=1.3&amp;content-type=text/vnd.viewcvs-markup">1.3</a></td>
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