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<p style="margin: 0px;">Ok I think I know where you are going with this.</p>
<p style="margin: 0px;">I started a small 2 nucleic acid system. I set RNA_Chain_A as the couple-moltype and couple-lambda0 and couple-lambda1 to vdw-q and none respectively. I then began a steep mdrun and got this error:</p>
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<p style="margin: 0px;">Program mdrun, VERSION 4.5<br />
Source code file: topsort.c, line: 112<br />
<br />
Fatal error:<br />
Function type Improper Dih. not implemented in ip_pert<br />
For more information and tips for troubleshooting, please check the GROMACS<br />
website at http://www.gromacs.org/Documentation/Errors</p>
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<p style="margin: 0px;">I have searched for this on google and found nothing. Do I need an Improper Dihedral section in my top/itp file?</p>
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<p style="margin: 0px;">Any help is much appreciated.</p>
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On September 14, 2010 at 4:24 AM Mark Abraham <mark.abraham@anu.edu.au> wrote:<br />
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----- Original Message -----<br />
From: TJ Mustard <mustardt@onid.orst.edu><br />
Date: Tuesday, September 14, 2010 10:54<br />
Subject: [gmx-users] FEP top file setup...<br />
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org><br />
<br />
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<p style="margin: 0px;"><span style="font-style: normal; font-weight: normal; background-color: #f5f8f0; font-size: 14px;">></span> I am tryng to run free energy perturbation (FEP) calculations on several ligands in several proteins. My problem is getting the correct B state atoms and charges for AMBER forcefields. If anyone can point me in the correct direction, that would be great.</p>
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<p style="margin: 0px;">I have read the Free Energy Tutorial from the Dill group wiki and found it very informative on how I should set up the top file and the experiment as a whole. But I can't seem to get the jobs to run correctly. I am assuming that the top file is incorrectly setup as the jobs run with lambda = 0.</p>
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It sounds to me more like your  .mdp might be wrong. Check out the FE section of manual 7.3<br />
<br />
Mark
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<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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