[EMAIL PROTECTED] wrote:
Hi,
All
I am running gromacs for simulation of 5 peptides. I have a problem with
the topology file in which the charge on each and every charge group is
not coming whole but in some of them it is in fraction which is not
correct. I have used G43a1 as well as OPLS but i am getting the same
problem with both of them. Now i don't know how to deal with it.
here is the part of topology file after pdb2gmx -f 1st.pdb -p 1st.top -o
1st.gro
in the example below the charge is integer after every residue. See
column with qtot.
Can anyone help me.
Thanks in Advance
ALKA
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB massB
1 opls_287 1 GLY N 1 -0.3 14.0067 ;
qtot -0.3
2 opls_290 1 GLY H1 1 0.33 1.008 ;
qtot 0.03
3 opls_290 1 GLY H2 1 0.33 1.008 ;
qtot 0.36
4 opls_290 1 GLY H3 1 0.33 1.008 ;
qtot 0.69
5 opls_292B 1 GLY CA 1 0.19 12.011 ;
qtot 0.88
6 opls_140 1 GLY HA1 1 0.06 1.008 ;
qtot 0.94
7 opls_140 1 GLY HA2 1 0.06 1.008 ;
qtot 1
8 opls_235 1 GLY C 2 0.5 12.011 ;
qtot 1.5
9 opls_236 1 GLY O 2 -0.5 15.9994 ;
qtot 1
10 opls_238 2 ASN N 3 -0.5 14.0067 ;
qtot 0.5
11 opls_241 2 ASN H 3 0.3 1.008 ;
qtot 0.8
12 opls_224B 2 ASN CA 4 0.14 12.011 ;
qtot 0.94
13 opls_140 2 ASN HA 4 0.06 1.008 ;
qtot 1
14 opls_136 2 ASN CB 5 -0.12 12.011 ;
qtot 0.88
15 opls_140 2 ASN HB1 5 0.06 1.008 ;
qtot 0.94
16 opls_140 2 ASN HB2 5 0.06 1.008 ;
qtot 1
17 opls_235 2 ASN CG 6 0.5 12.011 ;
qtot 1.5
18 opls_236 2 ASN OD1 6 -0.5 15.9994 ;
qtot 1
19 opls_237 2 ASN ND2 7 -0.76 14.0067 ;
qtot 0.24
20 opls_240 2 ASN HD21 7 0.38 1.008 ;
qtot 0.62
21 opls_240 2 ASN HD22 7 0.38 1.008 ;
qtot 1
22 opls_235 2 ASN C 8 0.5 12.011 ;
qtot 1.5
23 opls_236 2 ASN O 8 -0.5 15.9994 ;
qtot 1
24 opls_238 3 ASN N 9 -0.5 14.0067 ;
qtot 0.5
25 opls_241 3 ASN H 9 0.3 1.008 ;
qtot 0.8
26 opls_224B 3 ASN CA 10 0.14 12.011 ;
qtot 0.94
27 opls_140 3 ASN HA 10 0.06 1.008 ;
qtot 1
28 opls_136 3 ASN CB 11 -0.12 12.011 ;
qtot 0.88
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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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