[gmx-users] Molecule not minimized and NVT failure
sun.iba2 at gmail.com
Mon Apr 18 18:30:19 CEST 2016
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.
Sent from my iPhone
> On 18-Apr-2016, at 9:36 pm, Justin Lemkul <jalemkul at 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 A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
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