[gmx-users] charge distriburion
elham tazikeh
elham.tazikeh at gmail.com
Wed Dec 31 08:36:03 CET 2014
Dear Justin
thanks for your replys
one of my most important problem is choosing correct pdb
in RCSB , there is not any pdb that consist of *Aspirin *+ HSA...and in
literature, using of *2i30* as pdb
my question is; should we use *docking software* for adding real Aspirin on
HSA or we can adding *ACE group to pdb file (by hand*) or none of them?
finally, for pdb=2i30 , Atom section in my .itp file (produce by PRODRG0
was;
[ 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
by advising your good ideas, i saw in aminoacids.rtp for charge(s) and i
reached to below cherges:
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 SAL O1' 1 *-0.635* 15.9994 ;'
2 C 1 SAL C1' 1 *0.38* 12.0110 ;'
3 OM 1 SAL O2' 1 * -0.635* 15.9994 ;'
4 C 1 SAL C1 1 *0* 12.0110
5 CH2 1 SAL C6 1 *-0.1* 14.0270
6 CH2 1 SAL C5 1 *-0.1* 14.0270
7 CR1 1 SAL C4 2 *-0.1* 13.0190
8 CR1 1 SAL C3 2 *-0.1* 13.0190
9 C 1 SAL C2 2 * 0.15* 12.0110
10 OA 1 SAL O2 2 *-0.548* 15.9994
11 H 1 SAL H2 2 * 0.398* 1.0080
As showed in above table, the sum of chares are not still Zero (even with
assuming H s ring)
please watch to them and give me help...
on the other hand, there are 2 molecules of SAL in pdb file that which one
have 10 atoms and in .itp file i achieved 11 atoms.is this correct?
Regards
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