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Thank you for your kind reply. I am using gromacs version 3.2. <br>
Actually sir, I am going to use it for synthetic polymers not for the
proteins etc. I had taken a test model of polyethylene (5 repeat units)
and when I tried to convert .PDB file to .GRO and .TOP using command
'pdb2gmx', it gave me error as follows:<br>
Fatal error: Residue 'PE' not found in residue topology database<br>
This was the case with all the test model polymers I tried. <br>
I am stuck right now. Please help me out. Thanking you.<br>
<br>
Rahul Karyappa<br>
NCL, Pune<br>
India<br>
<br><font face="Arial" size="2"><TABLE STYLE="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD><b><i>-- Original Message --</i></b><br>From: David <spoel@xray.bmc.uu.se><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Date: Thu, 11 Aug 2005 09:08:23 +0200<br>Subject: Re: [gmx-users] files missing<br><br>On Thu, 2005-08-11 at 10:18 +0530, Rahul Karyappa wrote:<br>> <br>> Dear all,<br>> I ran x2top command to get .top file from .gro. But it gave me error<br>> for all the forcefields I used. The error was as follows:<br>> Fatal error: Library file ffG43a1.n2t not found in current dir nor in<br>> default directories.<br>> Also when I used other forcefields it gave me same errors but the file<br>> names were different i.e. ffG43b1.n2t, ffG43a2.n2t, ffoplsaa.n2t and<br>> ffgmx2.n2t.<br>> Please tell me where I can get these files. I have searched for these<br>> files on my pc (/usr/local/gromacs/share/top) but these are not there.<br>> Waiting for your kind reply.<br>> <br>> <br>> <br>> <br>> <br>> Rahul Karyappa<br>> NCL, Pune<br>> India<br>> <br>> *****************************************************************<br>> This email is virus free by TrendMicro Inter Scan Security Suite.<br>> *****************************************************************<br>> <br><br>Which gromacs version?<br>I'm attaching the ffgmx version. Are you sure you don't want to use<br>pdb2gmx (for proteins)?<br>-- <br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br>spoel@xray.bmc.uu.se spoel@gromacs.org http://xray.bmc.uu.se/~spoel<br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________<br>gmx-users mailing list<br>gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<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.</TD></TR></tbody></TABLE></font></BODY></HTML>
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