<HTML dir=ltr><HEAD><TITLE>Re: [gmx-users] modified atomtypes.atp and grompp</TITLE>
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<DIV dir=ltr><FONT face=Arial color=#000000 size=2>Dear Justin,</FONT></DIV>
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<DIV dir=ltr><FONT face=Arial size=2>I checked my working directory (including ff-directory) again and found some entries (i added myself) with the old uppercase spelling in the nonbonded.itp. After editing these lines everything works well. Conclusion: I have to learn using the command grep properly :)</FONT></DIV>
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<DIV dir=ltr><FONT face=Arial size=2>Thank you very much for your help.</FONT></DIV>
<DIV dir=ltr><FONT face=Arial size=2>Felix</FONT></DIV></DIV>
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<FONT face=Tahoma size=2><B>Von:</B> gmx-users-bounces@gromacs.org im Auftrag von Justin A. Lemkul<BR><B>Gesendet:</B> Fr 11.03.2011 13:07<BR><B>An:</B> Discussion list for GROMACS users<BR><B>Betreff:</B> Re: [gmx-users] modified atomtypes.atp and grompp<BR></FONT><BR></DIV>
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<P><FONT size=2>Rausch, Felix wrote:<BR>> <BR>> Dear Gromacs users,<BR>> <BR>> I would like so simulate a protein with phosphorylated amino acids with<BR>> Gromacs 4.5.3. To do so, I got the "ffG43a1p" forcefield available from<BR>> the user contributions section (subsection force fields) and adapted the<BR>> parameters given there to Gromos53a6.<BR>> The problem now is that they introduced a new atom type called "OP",<BR>> which I have to add to the atomtypes.atp of my modified force field. I<BR>> already read about problems of a modified atomtypes.atp here in the<BR>> mailing list, but I assumed the problems were sorted out with version 4.5.3.<BR><BR>Not entirely, but probably the post you saw related to an LP atomtype, which<BR>appears to be a special case.<BR><BR>> But if I add OP to the atom list, pdb2gmx works fine, but grompp is<BR>> raising the error<BR>> <BR>> Program grompp, VERSION 4.5.3.<BR>> Source code file: toppush.c, line: 629<BR>> <BR>> Fatal error:<BR>> Unknown atomtype CMET<BR>> <BR>> which is quite strange because "CMET" isn't appearing in any file I'm<BR>> using. When I remove OP from the atom list, pdb2gmx is of course raising<BR>> an error, so I'm a bit stuck here...<BR>> <BR><BR>grompp reads all the force field files and is finding something it doesn't like.<BR> In 4.5.3, the proper capitalization should be "CMet," not "CMET," as it was in<BR>old versions. Capitalization and other nomenclature has been standardized as of<BR>version 4.5.3, so old files with outdated names cause errors.<BR><BR>-Justin<BR><BR>> To cut a long story short: Is there any way to introduce a new atom type<BR>> to atomtypes.atp or do I have to parameterize the phosphorylated<BR>> residues with already presend atom types? <BR>> <BR>> Thank you in advance,<BR>> Felix Rausch<BR>><BR>> <BR>><BR><BR>--<BR>========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<BR>Department of Biochemistry<BR>Virginia Tech<BR>Blacksburg, VA<BR>jalemkul[at]vt.edu | (540) 231-9080<BR><A href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</A><BR><BR>========================================<BR>--<BR>gmx-users mailing list gmx-users@gromacs.org<BR><A href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read <A href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</A><BR></FONT></P></DIV></BODY></HTML>