Thank you Justin, I understand the problems with PRODRG. I am switching to ATB now but earlier, I performed similar study with different ligand using PRODRG, and corrected charges according to the mentioned paper. No problem occured at all. I understand all systems are different. I was surprised as the ligand is a very simple molecule. Anyhow, now I will rerun using ATB and will contact if the problem persists. Thank you Suniba
Sent from my iPhone > On 18-Apr-2016, at 9:36 pm, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> On 4/18/16 12:02 PM, suniba wrote: >> >> Hello users I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0. >> Therefore, following Justin's tutorial, I used PRODRG for ligand topolgy. I > > After doing my tutorial, you should *not* be using PRODRG for topologies, for > the reasons mentioned in that very tutorial. > >> have drawn ligand using chemdraw and minimized the structure using chem3D. >> However, during energy minimization step in gromacs, the values converge >> earlier after 490 steps of minimization. This means that structure is not >> energy minimized properly. Also, during NVT, it crashes very early giving a > > The number of steps has nothing to do with whether or not EM was effective. > >> LINCS warning which is posted frequently in mailing list and the 'water' >> molecule not settled error. I have gone through all the solutions and >> according to my knowledge, the problem is with minimization. I am confused >> now how to minimize the structure properly to avoid the error. The long bond >> warning might also arise due to bad minimization? Any suggestions please. If >> require I can paste the ligand co-ordinates. > > Ligand coordinates will tell us nothing of use. The topology is more > instructive, but in general go through: > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System > > If your topology is straight from PRODRG, that's suspect #1 on my list. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
