[gmx-users] md with multiple ligands

[Ansuman Biswas]

Dear gromacs users,

I wish to run a protein ligand md in Gromacs 4.5.3 with charmm force
field. Its a dimeric protein with a MG ion and 2 ligands bound to two
active sites. I wish to run the dimer and there would be 4 ligands. I
generated the topology files (.itp) of ligands using SWISSPARAM. Before
running the energy minimization I changed the topol.top file accordingly
as mentioned in the SWISSPARAM website. I added all the itp files
together.But while running GROMPP I got an error message like,


WARNING 1 [file ADP.itp, line 24]:
  Overriding atomtype NPYL


WARNING 2 [file ADP.itp, line 25]:
  Overriding atomtype C5A


WARNING 3 [file ADP.itp, line 26]:
  Overriding atomtype N5B


WARNING 4 [file ADP.itp, line 27]:
  Overriding atomtype C5B


WARNING 5 [file ADP.itp, line 28]:
  Overriding atomtype CB


WARNING 6 [file ADP.itp, line 29]:
  Overriding atomtype NPYD


WARNING 7 [file ADP.itp, line 30]:
  Overriding atomtype PO4


WARNING 8 [file ADP.itp, line 31]:
  Overriding atomtype O2CM


WARNING 9 [file ADP.itp, line 32]:
  Overriding atomtype OR


WARNING 10 [file ADP.itp, line 33]:
  Overriding atomtype CR


WARNING 11 [file ADP.itp, line 34]:
  Overriding atomtype NC=C


WARNING 12 [file ADP.itp, line 35]:
  Overriding atomtype HCMM


WARNING 13 [file ADP.itp, line 36]:
  Overriding atomtype HNCO


WARNING 14 [file ADP.itp, line 37]:
  Overriding atomtype HOCO


WARNING 15 [file ADP.itp, line 38]:
  Overriding atomtype HOR


WARNING 16 [file ADP.itp, line 43]:
  Overriding atomtype PO4


WARNING 17 [file ADP.itp, line 44]:
  Overriding atomtype O2CM


WARNING 18 [file ADP.itp, line 45]:
  Overriding atomtype OR


WARNING 19 [file ADP.itp, line 46]:
  Overriding atomtype CR


WARNING 20 [file ADP.itp, line 48]:
  Overriding atomtype HCMM


WARNING 21 [file ADP.itp, line 49]:
  Overriding atomtype HOR


WARNING 22 [file ADP.itp, line 50]:
  Overriding atomtype HOCO


WARNING 23 [file ADP.itp, line 52]:
  Overriding atomtype NC=O


WARNING 24 [file ADP.itp, line 53]:
  Overriding atomtype C=O


WARNING 25 [file ADP.itp, line 54]:
  Overriding atomtype N=C


WARNING 26 [file ADP.itp, line 55]:
  Overriding atomtype C=C


WARNING 27 [file ADP.itp, line 56]:
  Overriding atomtype PO4


WARNING 28 [file ADP.itp, line 57]:
  Overriding atomtype O2CM


WARNING 29 [file ADP.itp, line 58]:
  Overriding atomtype OR


WARNING 30 [file ADP.itp, line 59]:
  Overriding atomtype CR


WARNING 31 [file ADP.itp, line 60]:
  Overriding atomtype O=C


WARNING 32 [file ADP.itp, line 61]:
  Overriding atomtype HCMM


WARNING 33 [file ADP.itp, line 62]:
  Overriding atomtype HOCO


WARNING 34 [file ADP.itp, line 63]:
  Overriding atomtype HOR


WARNING 35 [file ADP.itp, line 64]:
  Overriding atomtype HOCC

Generated 25425 of the 25425 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 22285 of the 25425 1-4 parameter combinations

-------------------------------------------------------
Program grompp, VERSION 4.5.3
Source code file: toppush.c, line: 1071

Fatal error:
Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =
1, while at->nr = 40)

I know that the problem is related to the merging of 4 itp files.
Please let me how I should do that.

thanking you,
with regards,

Ansuman Biswas
C/O Prof K.Sekar
Dept.of Physics
Indian Institute of Science
Bangalore:560012
India


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