[gmx-users] Re: gmx-users Digest, Vol 106, Issue 68

[Ansuman Biswas]

>
> Message: 8
> Date: Wed, 13 Feb 2013 08:28:00 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] md with multiple ligands
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <511B94E0.4040800 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> 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
But according to SWISSPARAM website I can only add one ligand.itp file.
So, is it possible to add ligand1 and ligand2 itp files?

Will it be ok if I merge all the ligand pdbs and then get the combined itp
file using that from SWISSPARAM and follow the protocol for one ligand?

Ansuman
>
> --
> ========================================
>
> 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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> End of gmx-users Digest, Vol 106, Issue 68
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