On 12/5/12 11:46 AM, James Starlight wrote:
Justin,
So as I understood such problems might be with all proteins consisted
of prostetic groups ( Rhodopsin, myoglobin etc). Is there more trivial
way to obtain parametrized models of such proteins with gromacs force
fields if I have itp's of the prostetic groups made by external
software ?
In general, a prosthetic group that is not bound covalently is handled by .itp
files, anything covalently attached is handled by .rtp entries. If you have an
.itp file for a covalently bound compound, then you need to convert it to .rtp
using the contents of the .itp. After all, everything we're talking about is
topological information, just in different formats.
-Justin
Thanks for help
James
2012/12/5 Justin Lemkul <jalem...@vt.edu>:
On 12/5/12 11:19 AM, James Starlight wrote:
Justin,
The GFP protein consist of chromophore group which matured after
folding of that protein. That prostetic group is the cyclized
derivative of the Ser-Tyr-Gly peptide which is the part of the
alpha-helix of that protein surrounded by the beta-barell interiour.
So I want to make simulation of such protein consisted of covalently
bonded prostetic group. I've made parametrisation of that isolated
chromophore but couldn't integrate it into GROMOS force field because
aminoacids.rtp didnt work with ITP file produced by PRODRG. It's also
inportant that different mutants of GFP consist of different types of
that chromophores so manual conversion of the ITP to RTP formats in
each cases ( I'd like to simulate different mutants) would be very
routinely.
I don't know of a way to convert .itp files into .rtp entries, though it
could probably be done. The time investment in developing such a script may
not be worth it, since creating an .rtp entry is rather simple following the
guide in the manual and existing entries (i.e. amino acids). The choice
(script vs. manual effort in a text editor) is up to you. I've done similar
things with other people before, so it's certainly possible, though a bit
tedious, especially for the GFP chromophore since there are lots of atoms
involved. I worked with it several years ago and I simply did it by hand
using the parameters that were suggested to you earlier for CHARMM.
-Justin
James
2012/12/5 Justin Lemkul <jalem...@vt.edu>:
On 12/5/12 11:00 AM, James Starlight wrote:
Hi Bharat,
That simulation have been done in charmm program so the convertion
from charmm to gromacs would be more routinely for me.
I think it would be better if you describe exactly what you need help
with.
If it's a matter of having parameters in CHARMM format but not Gromacs
format, then all you need is to follow the manual to implement the
parameters. If you're having a specific problem along the way, please
describe it fully and specifically, otherwise the default response is
"everything's in the manual and elaborated on at the webpage you already
quoted."
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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.
Research Scientist
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.
Research Scientist
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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