Thanks Jason
That is indeed a very helpful script when I run it I get the following
error/warning:
ParmWarning: ATOMS_PER_MOLECULE section corrupt! Molecules are not
contiguous!
MissingDisulfide: Detected two cysteine residues whose sulfur atoms are
within 3
Angstroms. Rename CYS to CYX in the PDB file and use the
'bond' command in tleap to create the disulfide bond
The second one does not make any sense - I do have two cysteines but they
are more than 21 Å apart. The first one is the one that I have a problem
with.
my metal coordinated water molecule is rearranged by amber such that it is
connected after the na+ which are added to neutralize the system - I am not
quite sure where the order is broken. The unit is okay
Checking 'prt'....
Checking parameters for unit 'prt'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Any suggestions to figure out where the problem arises?
On Thu, Mar 19, 2015 at 11:34 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 19 2015 - 13:00:04 PDT
