Ok I know what the problem is but I do not know how to solve it or if can
be solved using PMEMD.mpi; when I add bonds between my metal ion and
histidine residues that are coordinating it I get the warning described :
ParmWarning: ATOMS_PER_MOLECULE section corrupt! Molecules are not
contiguous!
the parameter file for my zinc ion looks like this:
!!index array str
"ZNA"
!entry.ZNA.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
"ZN" "ZN" 0 1 131072 1 30 0.3846
!entry.ZNA.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
"ZN" "ZN" 0 -1 0.0
!entry.ZNA.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.ZNA.unit.childsequence single int
2
!entry.ZNA.unit.connect array int
0
0
!entry.ZNA.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
"U" 0 "R" 1
"R" 1 "A" 1
!entry.ZNA.unit.name single str
"ZNA"
!entry.ZNA.unit.positions table dbl x dbl y dbl z
0.0 0.0 0.0
!entry.ZNA.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
0 0 0 0 0 0
!entry.ZNA.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
"ZNA" 1 2 1 "?" 0
!entry.ZNA.unit.residuesPdbSequenceNumber array int
0
!entry.ZNA.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.ZNA.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
Is there a way to fix this or is there a mistake in my lib file for the
zinc ion?Any suggestions would be highly appreciated thanks
On Thu, Mar 19, 2015 at 12:51 PM, Jorgen Simonsen <jorgen589.gmail.com>
wrote:
> 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
>>>
>>
>>
>
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Received on Thu Mar 19 2015 - 15:30:03 PDT
