On 6/13/18 11:11 AM, nik...@tezu.ernet.in wrote:
On 5/31/18 10:54 AM, nik...@tezu.ernet.in wrote:
Hello,
Can anyone provide me with the correct topolgy file for
Adenosine-5'-Monophosphate(AMP).
AMP is part of the CHARMM36 force field. Generate the topology with
pdb2gmx.
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
------------------------------
Dear Justin,
Thanks a lot for your reply.
I have generated the topology using CHARMM36 forcefield.
But, however i would like to convert it into an itp file to
be used in gromos54a7 force field.
I am not being able to properly generate the itp file.
I have attached the topol.top file generated for AMP through CHARMM36 in
the link provided.
https://www.dropbox.com/s/uetrnnim4a30j01/topol.top?dl=0
You can't convert one force field to another. Force fields are
self-consistent entities. You have to choose one force field and stick
to it. If GROMOS96 doesn't meet your needs, then use a force field that
does, like CHARMM36.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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