On Thu, Mar 19, 2015 at 2:15 PM, Jorgen Simonsen <jorgen589.gmail.com>
wrote:
> Hi all,
>
> I am trying to run an NPT simulation using amber12. I have been able to
> minimize and heat the system but during the production run I get the
> following error:
>
> | ERROR: PMEMD does not support intermolecular PRFs!
>
> I have looked at the earlier threads on this subject and it seems to be
> related to bad prmtop - I am not quite sure how to debug that. I have added
> a custom water molecule, WAM, which I have covalently link to a metal site.
> I have triangulized the molecule with the following command:
>
> > # add additional bond to the water molecule
> set prt.332.H1 pert true
> set prt.332.H2 pert true
> > # H-H bond
> bond prt.332.H1 prt.332.H2
>
> first of all I am not sure what that error means ? Secondly, how to fix it.
> I know it is quite vague description at this point but I am not sure what
> the problem is - so I can run NVT simulations but I would like to fix this
> error as I fear it might be some underlaying issue in the prmtop.
>
Open the prmtop file in parmed.py and run the "checkValidity" command. If
it finds a problem, it will tell you how to fix it (if it can be fixed).
It's possible that you will have to reorder atoms to make molecules appear
contiguously. So I would suggest loading a coordinate file as well so that
you can write out both a prmtop and inpcrd file. So something like this:
parmed.py -i <input_file>
where <input_file> contains
parm your.prmtop
loadRestrt your.inpcrd
checkValidity
# if you are told to, do the following
setMolecules
# Write out both a prmtop and inpcrd
outparm fixed.prmtop fixed.inpcrd
Then try using fixed.prmtop and fixed.inpcrd for your simulations.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 19 2015 - 12:00:03 PDT
