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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