bipin singh wrote:
Thanks for your reply.
Yes, you are right that these topologies are self supporting and there
is no need to to call any other information. I followed your
suggestions and able to generate a biphasic system of water/octane
containing a protein molecule. But, when I tried grompp on this
biphasic system (containing octane+water+protein), it results in error
even if I include the topologies in forcefield.itp file.
The error was
Fatal error:
Atomtype hc not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
If you introduce a new atomtype in your topology somewhere (presumably in one of
the GAFF topologies), then you have to declare them in an [atomtypes] directive
in the appropriate place in the .top file. These types are case sensitive as
well. For dealing with GAFF-type topologies, assuming you can #include them
within whatever AMBER force field you've chosen (up to you to prove), you can do
something like:
#include "amberXX.ff/forcefield.itp"
#include "ligand.itp"
[ moleculetype ]
;name nrexcl
Protein 3
(etc)
The inclusion of the ligand topology (at this specific location) will add the
new [atomtypes] at the appropriate level of precedence, before any
[moleculetypes] are declared.
-Justin
On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul <jalem...@vt.edu> wrote:
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
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========================================
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
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========================================
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
========================================
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