On 2/13/13 5:24 AM, Ansuman Biswas wrote:
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.
The ligands probably use common atom types and each .itp file likely has an
[atomtypes] directive that introduces these new types. Probably the easiest
thing to do is create a merged [atomtypes] directive that lists all of the
necessary atom types so you don't list them separately in each file. One
approach that I have used in the past is to create an .itp file that only has
atom types in it, then call something like:
#include "charmm27.ff/forcefield.itp"
; only has [atomtypes]
#include "my_ligand_atomtypes.itp"
; these don't introduce [atomtypes] any more
#include "ligand1.itp"
#include "ligand2.itp"
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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