Dear gmx-users,
New pdb2gmx seems to be strange that
the net charge of the first group (N terminal) is not decimal number.
I put LEU-TRP-VAL.pdb (attached file) into pdb2gmx
and chose ffG53a6 for the force field.
In the topol.top (attached file) obtained,
the first and second charge groups are as follows:
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 33 LEU rtp LEU q +1.0
1 NL 33 LEU N 1 0.129 14.0067 ; qtot 0.129
2 H 33 LEU H1 1 0.248 1.008 ; qtot 0.377
3 H 33 LEU H2 1 0.248 1.008 ; qtot 0.625
4 H 33 LEU H3 1 0.248 1.008 ; qtot 0.873
5 CH1 33 LEU CA 2 0.127 13.019 ; qtot 1
6 CH2 33 LEU CB 2 0 14.027 ; qtot 1
I am sorry if I misunderstand it.
Best regards,
Shuntaro
LWV.pdb
Description: Binary data
topol.top
Description: Binary data
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