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Actually Sir, my structure contains aluminium and silicon atoms which
PRODRG does not support. And using pdb2gmx I get lots of errors. So by
running x2top command I can get .top file. But for x2top errors which I
have mentioned, how can I proceed?<br>
Waiting for your kind reply.<br>
<br>
Rahul Karyappa<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 van der Spoel <spoel@xray.bmc.uu.se><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Date: Sat, 26 Nov 2005 14:14:49 +0100<br>Subject: Re: [gmx-users] errors while runnning x2top command<br><br><br>Rahul Karyappa wrote:<br>> Dear all,<br>> I wanted to generate the topology file using x2top command. When I <br>> gave the command:<br>> x2top -f conf.gro -o out.top -r out.rtp -param<br><br>x2top is really a last resort for special cases. Have you tried pdb2gmx <br>(proteins) or the PRODRG server for small molecules?<br><br>> <br>> it gave me following error:<br>> Select the Force Field:<br>> 0: GROMOS96 43a1 Forcefield (official distribution)<br>> 1: GROMOS96 43b1 Vacuum Forcefield (official distribution)<br>> 2: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)<br>> 3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>> 4: Gromacs Forcefield (see manual)<br>> 5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use for new runs)<br>> 4<br>> Looking whether force field file ffgmx.rtp exists<br>> Opening library file /usr/local/gromacs/share/top/ffgmx.rtp<br>> Generating bonds from distances...<br>> Opening library file /usr/local/gromacs/share/top/ffgmx.atp<br>> There are 54 type to mass translations<br>> atom 615<br>> Opening library file /usr/local/gromacs/share/top/ffgmx.n2t<br>> There are 20 name to type translations<br>> Fatal error: No forcefield type for atom OA (4) with 4 bonds<br>> <br>> Where I need to make changes? Please help me out. I wanted to create a <br>> topology file. I started doing it manually but it is very time-consuming <br>> and also it is tedious job. Thanking you in advance.<br>> <br>> Rahul Karyappa<br>> <br>> *****************************************************************<br>> This email is virus free by TrendMicro Inter Scan Security Suite.<br>> *****************************************************************<br>> <br>> <br>> ------------------------------------------------------------------------<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.<br><br><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.<br><br>*****************************************************************<br>This email is virus free by TrendMicro Inter Scan Security Suite.<br>*****************************************************************<br></TD></TR></tbody></TABLE></font></BODY></HTML>
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