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 <jalem...@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 <jalem...@vt.edu<mailto: >> jalem...@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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > 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@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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