[gmx-users] invalid order of directive moleule type

merc mertens merc.mertens at gmx.net
Tue Nov 7 13:00:02 CET 2006

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" <harpreetsingh05 at hotmail.com>
An: gmx-users at 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 at 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 gmx-users-request at gromacs.org.
> 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

More information about the gromacs.org_gmx-users mailing list