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.
Thanks for any help or suggestions
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Received on Thu Mar 19 2015 - 11:30:04 PDT
