[gmx-users] invalid order of directive moleule type

[Tsjerk Wassenaar]

Hi Harpreet,

Regarding the message "invalid order ...", check the archives of this
mailing list. Further note that you shouldn't use the gmx (ffgmx)
force field, but should choose one of the Gromos force fields (united
atom), OPLS or Encad (all-atom).

Specific to your problem is that there is a mismatch between the names
of atoms in the .pdb file and the names in the residue database (.rtp)
file of the force field you chose. Usually, it's best to modify the
names in the .pdb file to match those in the .rtp file.

By the way, since you're new to Gromacs.., have you tried the
MD/Gromacs tutorial from the MD group in Groningen? If not, it may be
a good start to get to know gromacs. At present the Groningen group is
off the air, but I've mirrored the site at:

http://nmr.chem.uu.nl/~tsjerk/MDCourse/

Hope it helps,

Tsjerk

On 11/7/06, merc mertens <merc.mertens at gmx.net> wrote:
> 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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> >
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-- 
Tsjerk A. Wassenaar, Ph.D.
post-doc
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623