[gmx-users] md with multiple ligands

[Justin Lemkul]

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

========================================