[gmx-users] mdsimulation of drug enzyme complex
abhijit kayal
kayalabhijitiitd at gmail.com
Fri Apr 9 15:41:39 CEST 2010
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
Abhijit
On Fri, Apr 9, 2010 at 6:33 PM, Justin A. Lemkul <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>> 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> | (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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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