On 12/5/12 12:57 PM, James Starlight wrote:
Dear Gromacs Users!
In one of my study I investigate interactions of the cyclic
nucleotides (cGMP and cAMP) with some cyclic-nucleotide-binding
proteins. I'm modelling that complexes in the gromos 56a7 ff with the
parameters for ligands made by prodrg. So I'm not quite sure about
correctness of charge distributions of that cyclic nucleotides. E.g
below charges of my mollecule of cGMP (united atom modell) is present.
; nr type resnr resid atom cgnr charge mass
1 O 1 DRG O6 7 -0.211 15.9994
2 C 1 DRG C6 7 0.211 12.0110
3 NR 1 DRG N1 8 -0.360 14.0067
4 H 1 DRG H1 8 0.360 1.0080
5 C 1 DRG C2 1 0.298 12.0110
6 NT 1 DRG N2 6 -0.830 14.0067
7 H 1 DRG H22 6 0.415 1.0080
8 H 1 DRG H21 6 0.415 1.0080
9 NR 1 DRG N3 1 -0.298 14.0067
10 C 1 DRG C4 2 0.210 12.0110
11 C 1 DRG C5 2 0.096 12.0110
12 NR 1 DRG N7 2 -0.626 14.0067
13 CR1 1 DRG C8 2 -0.030 12.0110
14 HC 1 DRG H8 2 0.006 1.0080
15 NR 1 DRG N9 2 0.179 14.0067
16 CH1 1 DRG C1* 2 0.165 13.0190
17 OA 1 DRG O4* 3 -0.176 15.9994
18 CH1 1 DRG C4* 3 0.240 13.0190
19 CH1 1 DRG C5* 3 0.089 14.0270
20 OA 1 DRG O5* 3 -0.177 15.9994
21 P 1 DRG PAQ 9 1.360 30.9738
22 OA 1 DRG OAR 9 -0.797 15.9994
23 OM 1 DRG OAS 9 -1.539 15.9994
24 OA 1 DRG O3* 4 -0.160 15.9994
25 CH1 1 DRG C3* 4 0.160 13.0190
26 CH1 1 DRG C2* 5 0.150 13.0190
27 OA 1 DRG O2* 5 -0.548 15.9994
28 H 1 DRG H8M 5 0.398 1.0080
Have anobody else modelled the same cyclic nucleotides in gromos ff ?
Is there any particular reason you're using Gromos96 instead of say, AMBER or
CHARMM? The latter perform significantly better than Gromos.
I'd like to compare my itp's of ligands with another works :)
At quick glance and without knowing what the ligand you've shown actually is,
the charges look reasonable for the 43A1 parameter set, but I don't know which
you're trying to actually use - 56A7 doesn't exist as far as I know. Do you
mean 53A6 or 54A7? If so, the charges do not seem right.
-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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