On 12/6/12 2:39 AM, James Starlight wrote:
Justin,
Could you provide me with the example of the server where I could
obtain Gromac's itp topologies for the charmm ff? I know many such
servers which could be useful only for preparation systems for NAMD
program.
Google "CHARMM ligand topology in Gromacs" (without the quotes) - the first
result is what you're looking for.
By the way recently I've made parametrization of my cGMP molecule by
means of ATB server. In the below example you can see that the charge
distribution is differs from the PRODRG example of that molecule which
I've posted yesterday. Does that charge distribution more suitable for
the 54a force field?
Given that PRODRG generally produces very bad charges, just about anything is
better ;)
Nucleotide parameters already exist in 54A7, I don't see why you necessarily
have to create them from scratch. In general, these charges look pretty good,
but note that DGUA already exists and can describe most of your molecule
already. The cyclic part is the only trick, but the nucleobase parameters
should be the same in cGMP and DGUA, given the nature of Gromos96 parameterization.
-Justin
[ atoms ]
; nr type resnr resid atom cgnr charge mass total_charge
1 NT 1 _N4H N2 1 -0.832 14.0067
2 H 1 _N4H H22 1 0.416 1.0080
3 H 1 _N4H H21 1 0.416 1.0080 ; 0.000
4 NR 1 _N4H N1 2 -0.715 14.0067
5 H 1 _N4H H1 2 0.427 1.0080
6 C 1 _N4H C2 2 0.775 12.0110
7 NR 1 _N4H N3 2 -0.691 14.0067
8 C 1 _N4H C4 2 0.431 12.0110
9 NR 1 _N4H N9 2 -0.227 14.0067 ; 0.000
10 C 1 _N4H C8 3 0.220 12.0110
11 HC 1 _N4H H01 3 0.162 1.0080
12 O 1 _N4H O6 3 -0.556 15.9994
13 C 1 _N4H C6 3 0.669 12.0110
14 C 1 _N4H C5 3 0.026 12.0110
15 NR 1 _N4H N7 3 -0.521 14.0067 ; 0.000
16 OE 1 _N4H O4* 4 -0.429 15.9994
17 CH1 1 _N4H C1* 4 0.429 13.0190 ; 0.000
18 CH1 1 _N4H C4* 5 0.000 13.0190 ; 0.000
19 OA 1 _N4H O5* 6 -0.422 15.9994
20 P 1 _N4H PAQ 6 0.971 30.9738
21 OM 1 _N4H OAR 6 -0.613 15.9994
22 OA 1 _N4H O3* 6 -0.382 15.9994
23 OA 1 _N4H OAS 6 -0.617 15.9994
24 H 1 _N4H H03 6 0.497 1.0080
25 CH2 1 _N4H C5* 6 0.319 14.0270
26 CH1 1 _N4H C3* 6 0.247 13.0190 ; -0.000
27 CH1 1 _N4H C2* 7 0.200 13.0190
28 OA 1 _N4H O2* 7 -0.614 15.9994
29 H 1 _N4H H8M 7 0.414 1.0080 ; 0.000
James
2012/12/5 Justin Lemkul <jalem...@vt.edu>:
On 12/5/12 1:39 PM, James Starlight wrote:
Justin,
Indeed the force field is the 54a7 ( modiffied version of the 54a6).
The main reason of using GROMOS ff in that case was the topology of
ligands which could be easily created by means of prodrg or ATB. On
other hand I've never worked with the protein-ligand complexes in
charmm ff for instance.
Well, you get out what you put in. A recent paper
(dx.doi.org/10.1002/jcc.23055) showed that Gromos force fields performed
very poorly for simulating nucleic acids. There are others, but that's just
a recent one. If you're choosing a force field because it makes life easy,
be prepared to defend your results if they are of poor quality or defend a
lot of wasted time while you re-do the simulations :)
There are servers that produce CHARMM topologies and other programs that
will convert AMBER topologies into Gromacs format as well. I would suggest
you evaluate all the options available.
By the way is there any suitable builing blocks (implemented in the
rtp enties of the gromos ff) which could be used for charge
assignment?
That depends on the functional group. If it's also found in proteins, yes.
If not, then maybe but probably not.
-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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