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
-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
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
harpreet singh wrote:
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
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
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