if i were you, i would rather adapt my pdb file to an existing forcefield as ffgmx, than trying to generate a new forcefield that fits to your pdb with prodrug. the first option seems much easier to me. what i mean is, if you change the names of you FAD atoms to the ones you see in the *rtp they will be recognized by pdb2gmx.
-------- Original-Nachricht -------- Datum: Tue, 07 Nov 2006 11:35:47 +0000 Von: "harpreet singh" <[EMAIL PROTECTED]> An: gmx-users@gromacs.org Betreff: [gmx-users] invalid order of directive moleule type > Hi All, > I am new to this package and want your help. I am trying to use GROMACS to > study energy minimization and molecular dynamics for FAD molecule. I am > having the following problems. > 1. I tried to run pdb2gmx for PDB file for FAD downloaded from > http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl site. and used the > gromacs force field . The program gave the following error: - > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.hdb > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx-n.tdb > Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx-c.tdb > > Back Off! I just backed up fad_test.top to ./#fad_test.top.1# > Processing chain 1 (53 atoms, 1 residues) > There are 0 donors and 0 acceptors > There are 0 hydrogen bonds > ------------------------------------------------------- > Program pdb2gmx, VERSION 3.3.1 > Source code file: pdb2gmx.c, line: 393 > Fatal error: > Atom O1P in residue FAD 1 not found in rtp entry with 61 atoms > while sorting atoms > On comparing topology file (ffgmx.rtp) for FAD entry i was surpried to see > that it has atom type enteries OP1, OP2 instead of O1P, O2P in downloaded > PDB file (fad.pdb). Also atom type at number 23 was O in ffgmx.rtp (for > FAD) and O3P was missing in this file. I am attaching the files herewith. > > 2. I tried to make .top and .gro files (fad92.top and fad.gro > respectively) > ,using PRODRG2 server. and used them with grompp commad > > grompp -f em.mdp -c fad92.gro -p fad92.top -o fad92.tpr > > This resulted in the following error. > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7# > checking input for internal consistency... > calling /usr/bin/cpp... > processing topology... > Cleaning up temporary file gromppfYcUxi > ------------------------------------------------------- > Program grompp, VERSION 3.3.1 > Source code file: topio.c, line: 388 > > Fatal error: > Invalid order for directive moleculetype, file ""fad92.top"", line 15 > ------------------------------------------------------- > > "Oh, There Goes Gravity" (Eminem) > > Kindly guide me to solve this problem. > Thanks in advance > > Harpreet Singh > > _________________________________________________________________ > Use your PC to make calls at very low rates > https://voiceoam.pcs.v2s.live.com/partnerredirect.aspx > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php