On 12/29/14 2:31 AM, elham tazikeh wrote:
Dear Justin
i really appricite for your help
i want to tell all did work until now, again:
1.total charges in my topol.top was +2, then by genion, i added 2 CL to my
comlex (HSA+Aspirin)
2.My .itp file (produce by PRODRG) was(consist of 11 atoms) :
[ moleculetype ]
; Name nrexcl
SAL 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 SAL O1' 1 -0.765 15.9994 ;'
2 C 1 SAL C1' 1 0.354 12.0110 ;'
3 OM 1 SAL O2' 1 -0.765 15.9994 ;'
4 C 1 SAL C1 1 -0.027 12.0110
5 CH2 1 SAL C6 1 0.102 14.0270
6 CH2 1 SAL C5 1 0.101 14.0270
7 CR1 1 SAL C4 2 0.010 13.0190
8 CR1 1 SAL C3 2 0.010 13.0190
9 C 1 SAL C2 2 0.130 12.0110
10 OA 1 SAL O2 2 -0.191 15.9994
11 H 1 SAL H2 2 0.041 1.0080
This explains your previous observations. This isn't aspirin. It's salicylic
acid, albeit incorrect because it has two CH2 groups that should be aromatic.
It also uses united aromatic carbons, which is incorrect.
with topology file and .itp file, after grompp (for produce nvt.tpr)
i encounted to below error :
*system has non-zero total charge : -0.619999*
I don't know what could have happened here. The topology above sums to -1, as
it should.
3.as yor re mentioned, Aspirin has 17 atoms.
for charge distribution, i used of QM (NBO calculation) and my results was:
1 C -0.095205
2 C -0.077566
3 C -0.084684
4 C -0.028579
5 C -0.223106
6 C 0.198041
7 H 0.147099
8 H 0.106100
9 H 0.101762
10 H 0.117238
11 C 0.443312
12 O -0.318010
13 H 0.247465
14 O -0.341986
15 O -0.318846
16 C 0.312765
17 O -0.320346
18 C -0.281115
19 H 0.136126
20 H 0.139768
21 H 0.139765
these are estimated for* 2-acetoxy benzoic acid *alone (i dont know , must
be calculate for complex HSA+Aspirin or Aspirin alone?)
You can't do the whole complex with QM. Parametrization would be done on
aspirin alone, but as I said, you probably don't need to use QM here; you can
put the topology together from existing building blocks.
4. on the other hand, i tried to search in *aminoacids.rtp* file for
*gromos* force field , but saw only charges for ACE group(other aminoacids
and some solvents) and i could not find out the charges of all atoms in
Aspirin molecule.
Put it together from building blocks; it's very straightforward. The aromatic
ring C-H are the same for PHE and TYR. The carboxylate is the same for anything
with an acid (GLU, ASP, C-terminus). The ester parameters (and likely the C in
the ring to which it is connected) you have to get from the literature, as this
functional group is not included in the protein force field.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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