ok just check for the not solvated system and here I get no errors when I
evaluate the validity of the prmtop and inpcrd:
Adding prmtop apo_vacuum.prmtop to parm list. apo_vacuum.prmtop is the
active parm.
Loading restart file apo_vacuum.inpcrd
Determining validity of prmtop
1 total warnings
so somehow the order seems to change when it is solvated and that cause
problems. I am not sure how to fix that.
On Thu, Mar 19, 2015 at 12:31 PM, Jorgen Simonsen <jorgen589.gmail.com>
wrote:
> 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
>>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 19 2015 - 13:00:05 PDT
