[gmx-users] Molecule not minimized and NVT failure
sun.iba2 at gmail.com
Mon Apr 18 18:15:58 CEST 2016
I corrected the PRODRG charges according to the paper cited in tutorial. The final energy after EM was -5.6. Anyhow, I will visualize em results and then see what happens.
Sent from my iPhone
> On 18-Apr-2016, at 9:37 pm, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> The number of EM steps doesn't mean anything. The final energy can suggest
> that something sensible happened, but the values depend on what your system
> has in it. You also should visualize the result of the EM and see if that
> fits with your chemical knowledge. PRODRG charges often won't produce
> sensible results.
>> On Mon, Apr 18, 2016 at 6:03 PM suniba <sun.iba2 at gmail.com> 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 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 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.
>> With Regards
>> Sent from my iPhone
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