<div style="font-family: 'Times New Roman'; font-size: 16px;">Dear Srinivs,<br _moz_dirty="" />thank you for response. You are right I have already found the source of problem. I have used PEO to name the chain group and forgot that the same group holded for residues. <br _moz_dirty="" /><br _moz_dirty="" />Greetings<br _moz_dirty="" />Zuzana<br /><br /><span>Dňa 03/19/10, <b class="name">jampani srinivas </b> <jampanis@gmail.com> napísal:</span><blockquote cite="mid:2504b2e21003181715m5915cf07jb6b37b9ae1d66492@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><div>Dear Zuzana,</div>
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<div>Recently i have done similar selection, I have got this error only when i miss some atoms or when i have some atoms in both groups. I would suggest you to check your groups carefully or you can make indexes for these selections in VMD and check whether you are missing some atoms from both groups.</div>
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<div>Srinivs.<br /><br /><br /></div>
<div class="gmail_quote">On Thu, Mar 18, 2010 at 4:55 PM, Zuzana Benkova <span dir="ltr"><<a href="mailto:Zuzana.Benkova@savba.sk" title="Vložiť mail do Zuzana.Benkova@savba.sk">Zuzana.Benkova@savba.sk</a>></span> wrote:<br />
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">
<div style="font-family: 'Times New Roman'; font-size: 16px;">Dear GROMACS users,<br />I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong. <br /><br />
I want to compile a PEO chain centered in box of 2900 water molecules. <br /><br />In my md.mdp the relevant section is as follows<br />Tcoupl = nose-hoover<br />tc-grps = PEO SOL<br />tau_t = 0.1 0.1<br />
ref_t = 50 50<br />gen_vel = yes<br />gen_temp = 50 50<br /><br />I have generated an index file where I have defined the PEO group. The [ SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms. This matches with the gro file. I tried to prepare a tpr file using<br />
<br />grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p topol.top -o PEO18_2900TIP3P_50K<br /><br />and got message<br /><br />Program grompp, VERSION 4.0.3<br />Source code file: readir.c, line: 1050<br /><br />Fatal error:<br />
16 atoms are not part of any of the T-Coupling groups<br /><br />I tried the compilations with 4.0.3 and 4.0.5 versions but the message was the same. <br /><br /><br /> I would be really thankful for an advice which can move me further. Thank you in advance.<br />
<br />Zuzana<br /><br /><br /><br /></div><br />--<br />gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" title="Vložiť mail do gmx-users@gromacs.org">gmx-users@gromacs.org</a><br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br />
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J. Srinivasa Rao Ph.D.<br />Post-doctoral Research Associate<br />C/o Prof. Luis R Cruz Cruz<br />Computational Biophysics Group<br />Department of Physics<br />Drexel University<br />3141 Chestnut St<br />Philadelphia, PA 19104, USA.<br />
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