Dear Gromacs users
I have a very strange problem when using pdb2gmx in the gromacs 4.5.3. I
looked up the mailing list but I can't find something similar.
I have in a .pdb file a crystalline substrate consisting of Si particles.
By running in previous gromacs version (i.e. gromacs 3.3) :
*pdb2gmx -f name.pdb -p topol.top -o output.gro
*
I get the following result for the *topol.top *file*:*
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 SI 1 ZZZ D1 1 0 28.08 ; qtot
0
2 SI 1 ZZZ D2 2 0 28.08 ; qtot
0
3 SI 1 ZZZ D3 3 0 28.08 ; qtot
0
4 SI 1 ZZZ D4 4 0 28.08 ; qtot
0
5 SI 1 ZZZ D5 5 0 28.08 ; qtot
0
etc
which of course is normal, but by doing the same in gromacs 4.5.3,
the *topol.top
*file* *is the following:
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 1 ZZZ rtp ZZZ q 0.0
1 SI 1 ZZZ D1 1 0 28.08 ; qtot
0
2 O 1 ZZZ D2 2 0 1.48594e-41 ;
qtot 0
3 O 1 ZZZ D3 3 0 1.48594e-41 ;
qtot 0
4 O 1 ZZZ D4 4 0 1.48594e-41 ;
qtot 0
5 O 1 ZZZ D5 5 0 1.48594e-41 ;
qtot 0
etc
I have no idea where these O come from.
Did anyone have similar problems?
Best regards, Chrysostomos
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