Thank you David,
I have yet to check the energies in both but did use checkValidity in Parmed and my input to chamber:
> chamber -top top_all36_prot.rtf -param par_all36_prot.prm -toppar toppar_water_ions.str -toppar toppar_all36_prot_heme.str -psf ../split.trial/step6-neutralized.psf -crd ../split.trial/step6-neutralized.crd -box 81.20309,81.20309,81.20309
I have also read in the toppar_water_ions.str and toppar_all36_prot_heme.str using the -str flag and it gives the same result below.
the output:
Creating chamber topology file from PSF ../split.trial/step6-neutralized.psf, RTF files [top_all36_prot.rtf], PAR files [par_all36_prot.prm], and STR files [toppar_water_ions.str, toppar_all36_prot_heme.str]. Coords from ../split.trial/step6-neutralized.crd. Using CMAP. Box info [81.20309, 81.20309, 81.20309, 90.0, 90.0, 90.0]. GB Radius set mbondi.
CharmmWarning: Detected PSF molecule section that is WRONG. Resetting molecularity.
> checkValidity
Determining validity of prmtop
9 total warnings
ParmWarning: Unexpected type for %FLAG ANGLE_FORCE_CONSTANT: expected float, but
got int
ParmWarning: Unexpected type for %FLAG DIHEDRAL_FORCE_CONSTANT: expected float,
but got int
ParmWarning: Unexpected type for %FLAG DIHEDRAL_PERIODICITY: expected float, but
got int
ParmWarning: Unexpected type for %FLAG SOLTY: expected float, but got int
ParmWarning: Unexpected type for %FLAG JOIN_ARRAY: expected int, but got float
ParmWarning: Unexpected type for %FLAG IROTAT: expected int, but got float
ParmWarning: Unexpected type for %FLAG BOX_DIMENSIONS: expected float, but got
int
NonUniversalWarning: Modified off-diagonal LJ parameters detected
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
These warnings I am not competent yet to investigate and the last confuses me to no end seeing that the closes 2 cystines (and only cystines) are at least 27Ang apart....
What is happening to cause this? Is my input improper?
Thank you for the help!
Best wishes,
Korey
________________________________________
From: David A Case [david.case.rutgers.edu]
Sent: Friday, October 07, 2016 8:55 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Best practice for charmm to AMBER conversion with HEME group
On Thu, Oct 06, 2016, Korey M Reid wrote:
>
> I have been successful in producing psf and crd files in charmm and
> perform minimization of input structure with missing atoms followed
> by solvation then minimization of the new system. The resulting psf
> and crd files were then read into the ParmEd program using the chamber
> command.
>
> With the output of ParmEd using parmout I am able to minimize my system,
> perform NVT heating over 20ps, I however cannot heat over a longer
> period of time and have my temperature not blow up,
First thing to do is to check the initial energies on the Amber side: if
the coordinates are the same as you used for CHARMM, make sure that the
energies reported by the two programs are (nearly) identical. If so,
run a short energy minimization in both programs: the details won't be
exactly the same, but you should get very similar results on both sides.
Also, use the checkstructure command in cpptraj to look for problems in the
prmtop files. (Also try the checkValidity command in parmed.) These will
identify some (certainly not all) possble problems with the CHARMM->Amber
conversion.
...good luck...dac
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Received on Fri Oct 07 2016 - 16:30:02 PDT
