Thanks for your reply. Yes, the earlier frame looks fine. When I used
use_sander=1 in &general section, I got the error as NATOM mismatch in
coordinate and topology file, so I generated complex, receptor, and ligand
topology files from the complex-solvated.parm7 using ante-MMPBSA. Now it
works fine.
Now I have another doubt, during the ante-MMPBSA I stripped water molecules
and also the counter ions (Cl-) which were used to neutralize the receptor.
Is that fine? because the complex-solvated.parm7 will contain the Cl- ions
but not the complex.parm7 and receptor.parm7. Is that necessary to
incorporate the counter ions if they are not in the binding pocket?
On Fri, Mar 8, 2019 at 7:36 PM David A Case <david.case.rutgers.edu> wrote:
> On Fri, Mar 08, 2019, Rinsha Chk wrote:
>
> >I am doing MMPBSA.py calculation using Amber16 and AmberTools 16. Each
> time
> >I encountered the following error :
> >
> >
> >VDWAALS = -nan EEL = -nan EGB =
> nan
> > 1-4 VDW = 1535.5730 1-4 EEL = 14130.9250 RESTRAINT =
> >0.0000
> > ESURF = 0.0000
> >
> >Processing frame 8
> > eff.c(2717) enb14 --> 1526.827
> > eff.c(2718) eel14 --> 14098.639
> > eff.c(2776) enb --> -nan
> > eff.c(2777) eel --> -nan
> >
>
> Do the earlier frames look OK? It looks like you have atoms on top of
> each other in frame 8. Use the "check" command in cpptraj to get more
> information. What happens in you skip frame 8?
>
> ....dac
>
>
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>
--
Rinsha. C H
Research Scholar
Theoretical and Computational Chemistry Lab
Department of Chemistry
NIT Calicut
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Received on Fri Mar 08 2019 - 06:30:05 PST
