VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Jun 04 2007 - 18:18:45 CDT

Do the following:

pdbalias the residue types (DISU to CYS, ASPP to ASP, GLUP to GLU)
pdbalias the appropriate atom types

(see the NAMD tutorial or psfgen manual for the appropriate use of
the pdbalias command)

Then, after you build your segments, apply the appropriate patches
(i.e. patch DISU ___ ___, again, see the psfgen manual and the
topology file for the appropriate use of the patch command).

Still do a guesscoord at the end. You should know it worked when no
atoms are discarded by the "coordpdb" command and zero coordinates
have to be guessed.

Let us know if this isn't clear enough.

On Jun 1, 2007, at 11:55 PM, Raul Araya wrote:

> Dear VMD users:
>
> This is a long question:
>
> I am working with electrostatic potential and MMPBSA calculations
> with a protein at pH 7 and 6.0 so in order to obtain the pH efect
> on the protonation state of the residues of the protein I'm using
> PRO-PKA and PDB2PQR in standalone mode, but later I want to create
> psf files with PSF_GEN/VMD to use the resulting files on NAMD. The
> problem goes as follow:
>
> --The PQR file I get is made with the CHARMM force field and CHARMM
> names for atoms and residues, so the CYS atoms that are involved in
> SS bonds are named as 1CB and 1SG and in the residue ID column the
> DISU name appears
> --For some protonated ASP the HD2 hydrogen is added and the ASPP
> name appears for some atoms in the RES-ID column (the same for the
> GLU protonated with the name GLUP).
> --The problem is that when I want to generate the PSF files with
> psfgen from VMD if I apply patches there are some atoms for which
> psfgen cannot assign coordinates, also in some cases is unable to
> recognize the ASPP or DISU names
> --So my question is should I?
> 1) rename those residues to read CYS instead of DISU
> and CB instread of 1CB and the assing patches for them (the same
> for the ASSP --> ASP and GLUP --> GLU) and run psfgen without
> guesscoord command ??
> 2) create pdbs without Hydrogens and then rename the
> residues and then remane the atoms and residues, apply psfgen with
> patches and guesscoord ??
>
> --Or any other suggestion ???
>
> Please Help, if the idea or question is not well understood or
> explained, please let me know because this is very important for me
> and I want to ask for help in the most clear way...
>
> Thanks
> Raul Araya
> Universidad de Chile.
>