[gmx-users] invalid order of directive moleule type

[harpreet singh]

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