hazizian wrote:
Hi
my ligand is Arginine (so it is not neccessary to use PRODRG )and the OPLS
forcefield of gromacs make the itp file of it. I check and all the atoms
present in the ligand itp file.There is no missing atom in the file.
atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_287 1 ARG N 1 -0.3 14.0067 ; qtot
-0.3
2 opls_290 1 ARG H1 1 0.33 1.008 ; qtot
0.03
3 opls_290 1 ARG H2 1 0.33 1.008 ; qtot
0.36
4 opls_290 1 ARG H3 1 0.33 1.008 ; qtot
0.69
5 opls_283 1 ARG CA 1 0.04 12.011 ; qtot
0.73
6 opls_140 1 ARG HA 1 0.06 1.008 ; qtot
0.79
7 opls_136 1 ARG CB 2 -0.12 12.011 ; qtot
0.67
8 opls_140 1 ARG HB1 2 0.06 1.008 ; qtot
0.73
9 opls_140 1 ARG HB2 2 0.06 1.008 ; qtot
0.79
10 opls_308 1 ARG CG 3 -0.05 12.011 ; qtot
0.74
11 opls_140 1 ARG HG1 3 0.06 1.008 ; qtot
0.8
12 opls_140 1 ARG HG2 3 0.06 1.008 ; qtot
0.86
13 opls_307 1 ARG CD 4 0.19 12.011 ; qtot
1.05
14 opls_140 1 ARG HD1 4 0.06 1.008 ; qtot
1.11
15 opls_140 1 ARG HD2 4 0.06 1.008 ; qtot
1.17
16 opls_303 1 ARG NE 5 -0.7 14.0067 ; qtot
0.47
17 opls_304 1 ARG HE 5 0.44 1.008 ; qtot
0.91
18 opls_302 1 ARG CZ 5 0.64 12.011 ; qtot
1.55
19 opls_300 1 ARG NH1 6 -0.8 14.0067 ; qtot
0.75
20 opls_301 1 ARG HH11 6 0.46 1.008 ; qtot
1.21
21 opls_301 1 ARG HH12 6 0.46 1.008 ; qtot
1.67
22 opls_300 1 ARG NH2 7 -0.8 14.0067 ; qtot
0.87
23 opls_301 1 ARG HH21 7 0.46 1.008 ; qtot
1.33
24 opls_301 1 ARG HH22 7 0.46 1.008 ; qtot
1.79
25 opls_271 1 ARG C 8 0.7 12.011 ; qtot
2.49
26 opls_272 1 ARG O1 8 -0.8 15.9994 ; qtot
1.69
27 opls_272 1 ARG O2 8 -0.8 15.9994 ; qtot
0.89
So for neutralizing I break 0.11 charge to 8 number of 0.01 charge and 6
number of 0.005 cherge and add them to 8+3=11 H atoms. so the total charge
of my ligand is +1.Is it correct way to solve this problem in the case that
I could not find any missing atom in ligand topology file?
No. When using pdb2gmx, how did you specify the N- and C-termini? Did you just
indicate NH3+ and COO-? If so, this is incorrect. You have to use the
zwitterionic options (since you are indeed dealing with a zwitterion).
The broken charge comes from this mistake.
If you ever find yourself with a fractional charge, do not get creative about
how to interpret it.
-Justin
Tehran University of Medical Sciences
www.tums.ac.ir
--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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