Thanks for the valueable suggessions, but sir i am actually want to use this
program for small molecules. I have taken single FAD molecule as u
suggested modified the atom type as described in ffgmx.rtp, program results
top and gro files using pdb2gmx, but while running grompp i am getting the
error:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
WARNING 1 [file "fad.top", line 128]:
No default Bond types, using zeroes
WARNING 2 [file "fad.top", line 139]:
No default Bond types, using zeroes
WARNING 3 [file "fad.top", line 141]:
No default Bond types, using zeroes
WARNING 4 [file "fad.top", line 328]:
No default Angle types, using zeroes
WARNING 5 [file "fad.top", line 329]:
No default Angle types, using zeroes
WARNING 6 [file "fad.top", line 334]:
No default Proper Dih. types, using zeroes
WARNING 7 [file "fad.top", line 336]:
No default Proper Dih. types, using zeroes
WARNING 8 [file "fad.top", line 338]:
No default Proper Dih. types, using zeroes
WARNING 9 [file "fad.top", line 341]:
No default Proper Dih. types, using zeroes
WARNING 10 [file "fad.top", line 343]:
No default Proper Dih. types, using zeroes
Cleaning up temporary file gromppLLm3l8
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: fatal.c, line: 416
Fatal error:
Too many warnings, grompp terminated
-------------------------------------------------------
"I Need Love, Not Games" (Iggy Pop & Kate Pierson)
Moreover , suppose if we want to use this program (grompp) for say, a
molecule which has no entry in any .rtp file provided with Gromacs and we
use the PRODRG server, then how to deal with the error "invalid molecular
directive type".
Kindly explain me regarding this error in detail, if you can spare some time
for me.
If you want i can give the sample files for what i am trying to do.
Thanks
From: "merc mertens" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] invalid order of directive moleule type
Date: Tue, 07 Nov 2006 13:00:02 +0100
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" <[EMAIL PROTECTED]>
An: gmx-users@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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