[gmx-users] mdsimulation of drug enzyme complex
Justin A. Lemkul
jalemkul at vt.edu
Fri Apr 9 15:54:55 CEST 2010
abhijit kayal wrote:
> Hi Justin,
> No my ligand is different. And my topolgy look like this
> #include "ffG43a1.itp"
> #include "rrg.itp"
> #include "drg.itp"
> and at the end it is like this
>
> Protein 1
> RRG 1
> DRG 1
> SOL 17662
> But I cannot understand where my topology is wrong.
> What I did is that I docked a ligand at active site then
> another ligand at the active site. Then I separate the ligands
> coordinate and generate .gro,.itp file using PRODRG server.
> Please reply
Since you have two different ligands, you will inherently have two
[moleculetype] definitions, between which no bonded interactions can be
specified. You should take another look at the atoms mdrun is complaining
about; I see no possible way that they can belong to atoms of different molecules.
To ultimately solve the problem, refer to the "blowing up" link I provided
before. Something about your model physics (parameters, .mdp settings, etc) is
unrealistic.
-Justin
>
> Abhijit
>
>
>
> On Fri, Apr 9, 2010 at 6:33 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> abhijit kayal wrote:
>
> Hi
> Thank you for your quick reply. As you mentioned I went
> through the mailing list search. And I am thinking my error
> occured at the system preparation with taking the two ligands.
> Earlier I ran md simulation taking the ligand individually and
> it was showing no error. So the topolgy I got from the PRODRG
> server is fine. So input file may
>
>
> Be prepared to justify that the topology is "fine" to a reviewer.
> Every time I have generated a PRODRG topology, some aspect of its
> atom types, charges, or charge groups has been wrong. You always
> need to prove your parameters are valid (hence the link I posted) or
> else you are wasting a lot of time doing meaningless MD with a
> flawed physical model.
>
>
> be error because GROMACS took both drug as a single one. So
> please help me how to take the input pdb file that it does not
> take a single ligand.
>
>
> I have no idea. Are your ligands different? The same? If they're
> the same, then there is absolutely no reason why you can't simply:
>
> #include "ligand.itp"
>
> [ molecules ]
> LIG 2
>
> Without seeing your topology or getting a better sense of what it is
> you did, there's not much more to offer. GROMACS isn't magically
> converting one molecule into two; somehow the instructions you're
> providing grompp and/or mdrun are causing the problem.
>
> -Justin
>
> On Fri, Apr 9, 2010 at 5:46 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> abhijit kayal wrote:
>
> Hello everybody,
> I am going to simulate an enzyme
> complex
> taking a ligand at active site and another ligand at
> allosteric
> site. When I ran md simulation taking ligand at active
> site only
> then it was ok. But when I am running the simulation
> taking both
> the ligand it is showing error "1-4 interaction between
> 3481 and
> 3485 at distance 4.979 which is larger than the 1-4 table
> size
> 2.000 nmThese are ignored for the rest of the simulation.This
> usually means your system is exploding,if not, you should
> increase table-extension in your mdp file or with user tables
> increase the table size". When I look the particular
> atoms they
> corrospond to the last atom of the ligand at the active site
> and the fourth atom the ligand at the allosteric site. So
> I can
> not understand why GROMACS takes into account bcause they are
> far apart or is there any wrong to my pdb file. I am
> genereting
> the coordinate and topology using PRODRG server. I am also
> attached my input pdb file.
>
> Please help me to find out the problem.
>
>
>
> Have you looked into the list archive? This "blowing up"
> error has
> been reported, diagnosed, and solved hundreds (if not
> thousands) of
> times, and there are only a few reasons why it's happening.
> Also:
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>
> >From your description, it sounds as if the topology is
> constructed
> incorrectly, since your two separate ligands are being considered
> one molecule and thus experiencing intramolecular 1-4
> interactions.
> Also note (as I've said dozens of times), face-value PRODRG
> topologies are often unsatisfactory (and thus unreliable) without
> modification of charges and charge groups. See here:
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> -Justin
>
>
>
> Abhijit
>
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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