[gmx-users] invalid order of directive moleule type

[merc mertens]

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
> 
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