On 2/14/13 1:20 AM, Ansuman Biswas wrote:
---------------------------- Original Message ----------------------------
Subject: Re: gmx-users Digest, Vol 106, Issue 68
From: ansuman@localhost
Date: Thu, February 14, 2013 10:16 am
To: gmx-users@gromacs.org
--------------------------------------------------------------------------
Message: 8
Date: Wed, 13 Feb 2013 08:28:00 -0500
From: Justin Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] md with multiple ligands
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <511b94e0.4040...@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.
Just a guess, but it's probably because each ligand.itp file introduces new atom
types which give the conflicts above.
So, is it possible to add ligand1 and ligand2 itp files?
Sure, my method should work. Please try it. I have done the exact same thing
with Amber topologies from acpype.
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?
Merging the coordinate files will probably not work. If you have multiple
molecules, you need multiple topologies.
-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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
