[gmx-users] atom name 1 in topol.top and conf.gro does not match

[Chang Woon Jang]

Dear Gromacs Users,

   I am trying to build topology file containing two different molecules (A
molecule, and B molecule)

"A" and "B" molecule contain three beads each. "A" molecules start from 1
to 600, and then "B" molecules start from 601 to 900 in conf.gro file.

I created topol.top file (this is coarse grained topology) as follow but it
does not properly worked.
The gromacs seems to read only "A" molecule.

Would you please let me know where the problem is?

Thank you very much.


[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
  1             1               no              0.0     0.0

[ atomtypes ]
;type    mass    charge       ptype          sigma      epsilon
 B     42.080999  0.000       A        1.000000000  1.000000000
 A     151.18579  0.000       A        1.000000000  1.000000000
 D     100.16139  0.000       A        1.000000000  1.000000000
 C     74.103099  0.000       A        1.000000000  1.000000000

[ moleculetype ]
; Name          nrexcl
Other_chain_A   3

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 A 2 Other_chain_A A1 1 0.000000 151.18579
2 A 2 Other_chain_A A2 2 0.000000 151.18579
3 B 2 Other_chain_A B1 3 0.000000 42.080999

[ bonds ]
1 3   8   1 1.0; 1:bond:1
2 3   8   1 1.0; 1:bond:2

[ angles ]
1 3 2   8  1 1.0  ; 1:angle:1

[ moleculetype ]
; Name          nrexcl
Other_chain_B   3

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 C 201 Other_chain_B C1 4 0.000000 74.103099
2 D 201 Other_chain_B D1 5 0.000000 100.16139
3 C 201 Other_chain_B C2 6 0.000000 74.103099

[ bonds ]
1 2   8   1 1.0  ; 1:bond:1
2 3   8   1 1.0  ; 1:bond:2

[ angles ]
1 2 3   8  1 1.0 ; 1:angle:1

[ system ]
; Name
Built with Packmol

[ molecules ]
; Compound        #mols
Other_chain_A       200
Other_chain_B       100



Best regards,
Changwoon Jang,