bipin singh wrote:
Thanks for your reply.
But as far as I understood, in order to use these GAFF topology (for
e.g. to perform simulation using these topologies) with Gromacs we
have to incorporate the information from these topologies to the
existing Amber forcefields in Gromacs or Is there anyway (Possibility
of using Standalone GAFF parameters in Gromacs) to do it without
performing this task.
As David said, the topologies stand on their own. You do not need to call any
further information from anywhere. The .top that you downloaded begins with a
[defaults] directive, declares atom types, and proceeds through the rest of the
topology with explicit parameters.
As you said these topologies are self supporting and we do not need to
change ffbonded.itp, but during grompp I got the following error, may
be because I have not added the dihedral information.
ERROR [file oct.top]:
No default Proper Dih. types
Please provide your suggestions.
I certainly don't see how this could have happened. All the dihedral parameters
are listed explicitly. The fatal error should have printed a line number in the
.top that is problematic, so start by investigating there. If you have modified
the topology in any way, then undo the changes and try again.
I did not have any trouble using this .top in an unmodified form, so I suspect
you've altered it in some way that has broken it.
-Justin
On Mon, Mar 26, 2012 at 17:29, David van der Spoel <sp...@xray.bmc.uu.se> wrote:
On 2012-03-26 13:55, bipin singh wrote:
Hello all,
I am using the GAFF topology provided for octan-1-ol at Gromacs liquid
database (http://virtualchemistry.org/molecules/111-87-5/index.php). I
have incorporated all the parameters
for atoms, bonds and non-bonded interaction type in the forcefield
(Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but I
am not sure how to add the dihedraltypes information in ffbonded.itp
from the GAFF topology as to add this information I need the phase and
kd for each dihedral. Is this information is available in the GAFF
topology provided in the Gromacs database ?
This topology is self supporting and you do not need anything else in
ffbonded.itp.
You should be careful merging such parameters with an existing force field,
because strictly speaking these are different force fields.
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
