parto haghighi wrote:
Dear GMX users,
I could make topology file of a ligand molecule by PRODRG but it has
wrong charge on each atom and as mentioned in Gromacs tutorial
(protein-ligand complex) I have used quantum mechanic calculation (like
spartan) to correct its charge:
.itp file from PRODRG:
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CAA 1 0.092 15.0350
2 CH2 1 DRG CAI 1 0.107 14.0270
3 NL 1 DRG N 1 0.702 14.0067
4 H 1 DRG H 1 -0.007 1.0080
5 CH2 1 DRG CAJ 1 0.106 14.0270
6 CH3 1 DRG CAB 2 0.071 15.0350
7 CH2 1 DRG CA 2 0.089 14.0270
8 C 1 DRG C 2 0.343 12.0110
9 O 1 DRG O 2 -0.733 15.9994
10 N 1 DRG NAL 2 0.120 14.0067
11 H 1 DRG HKL 2 -0.009 1.0080
12 C 1 DRG CAP 2 0.119 12.0110
13 C 1 DRG CAN 3 -0.037 12.0110
14 CH3 1 DRG CAC 3 0.047 15.0350
15 CR1 1 DRG CAG 3 -0.020 12.0110
16 HC 1 DRG HAN 3 0.013 1.0080
17 CR1 1 DRG CAF 3 -0.020 12.0110
18 HC 1 DRG HAM 3 0.013 1.0080
19 CR1 1 DRG CAH 3 -0.020 12.0110
20 HC 1 DRG HAO 3 0.013 1.0080
21 C 1 DRG CAO 3 -0.036 12.0110
22 CH3 1 DRG CAD 3 0.047 15.0350
.itp file whit modification based on Hatree-Fock quantum chemical
calculations using 6-31* basis set:
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CAA 1 -0.507 15.0350
2 CH2 1 DRG CAI 1 0.117 14.0270
3 NL 1 DRG N 1 0.372 14.0067
4 H 1 DRG H 1 0.391 1.0080
5 CH2 1 DRG CAJ 1 0.104 14.0270
6 CH3 1 DRG CAB 2 -0.512 15.0350
7 CH2 1 DRG CA 2 -0.368 14.0270
8 C 1 DRG C 2 0.983 12.0110
9 O 1 DRG O 2 -0.656 15.9994
10 N 1 DRG NAL 2 -0.689 14.0067
11 H 1 DRG HKL 2 0.391 1.0080
12 C 1 DRG CAP 2 -0.105 12.0110
13 C 1 DRG CAN 3 0.367 12.0110
14 CH3 1 DRG CAC 3 -0.700 15.0350
15 CR1 1 DRG CAG 3 -0.364 12.0110
16 HC 1 DRG HAN 3 0.189 1.0080
17 CR1 1 DRG CAF 3 -0.079 12.0110
18 HC 1 DRG HAM 3 0.159 1.0080
19 CR1 1 DRG CAH 3 -0.412 12.0110
20 HC 1 DRG HAO 3 0.202 1.0080
21 C 1 DRG CAO 3 0.425 12.0110
22 CH3 1 DRG CAD 3 -0.739 15.0350
.itp file of a reference (dynamic and structural properties of lidocaine
in lipid bilayer,Carl-Johan Högberg, Arnold Maliniak, Alexander P.
Lyubartsev ⁎ http://www.elsevier.com/locate/biophyschem ):
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CAA 1 0.025 15.0350
2 CH2 1 DRG CAI 1 0.248 14.0270
3 NL 1 DRG N 1 0.049 14.0067
4 H 1 DRG H 1 0.405 1.0080
5 CH2 1 DRG CAJ 1 0.248 14.0270
6 CH3 1 DRG CAB 2 0.025 15.0350
7 CH2 1 DRG CA 2 0.000 14.0270
8 C 1 DRG C 2 0.227 12.0110
9 O 1 DRG O 2 -0.411 15.9994
10 N 1 DRG NAL 2 0.088 14.0067
11 H 1 DRG HKL 2 0.008 1.0080
12 C 1 DRG CAP 2 0.088 12.0110
13 C 1 DRG CAN 3 -0.004 12.0110
14 CH3 1 DRG CAC 3 0.030 15.0350
15 CR1 1 DRG CAG 3 -0.013 12.0110
16 HC 1 DRG HAN 3 1.0080
17 CR1 1 DRG CAF 3 -0.013 12.0110
18 HC 1 DRG HAM 3 1.0080
19 CR1 1 DRG CAH 3 -0.013 12.0110
20 HC 1 DRG HAO 3 1.0080
21 C 1 DRG CAO 3 -0.005 12.0110
22 CH3 1 DRG CAD 3 0.022 15.0350
I have tried all of them several times but they are very different from
each other.
What can I do? and when I use for example spartan to calculate charges
how can I select which one of methods are the best ? what is the
reliable reference to compare my result with?
QM calculations are the starting point, not the end, for Gromos96
parameterization. There are some recommendations here in a paper we published
some time ago (http://pubs.acs.org/doi/abs/10.1021/ci100335w). Since most of
the functional groups in lidocaine are present in the Gromos96 force field
already, assigning charges by chemical analogy makes sense. The only
complication is the tertiary N.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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