[gmx-users] invalid order of directive moleule type

harpreet singh harpreetsingh05 at hotmail.com
Tue Nov 7 12:35:47 CET 2006

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 

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