Re: Generate PSF structure

From: Tim Isgro (timisgro_at_ks.uiuc.edu)
Date: Tue Mar 09 2004 - 10:24:01 CST

Hi Peter,

First off, your psfgen script should change the resname HIS in the pdb to
something that the topol file regocnizes (either HSP, HSE, HSD based on
which protonation state you think histidine is in). alias residue HIS
HSE.

You should break the system up by writing pdb's for the protein, lipid,
and water (using VMD if you wish) so that you may generate separate
segments of each with psfgen.

The entries for DPPC in the topol file are a little annoying. They
separate a single molecule into 4 residues/patches (PALM, PCGL, EST1,
EST2). Thus, change residue names for partiucular atoms from DPP (in your
pdb) to something else (say PCG for the PCGL atoms) and use alias residue
PCG PCGL in your psfgen script. VMD can change the resname for a set of
atoms you select.

Should work,
Tim

On Mon, 8 Mar 2004, Peter Spijker wrote:

> Hi Brian, and others,
>
> This is the (reduced) error I encounter. Thanks for helping.
>
> Greetz,
>
> Peter
>
> ---
>
> PSFGEN from NAMD 2.5 for Linux-i686
> reading topology file top_all27_prot_lipid.inp
>
> >>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
> >>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
> from
> >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
> >>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
> >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
> and
> \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
> \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
> Alexander D. MacKerell Jr.
> August 1999
> All comments to ADM jr. email: alex,mmiris.ab.umd.edu
> telephone: 410-706-7442
>
> Created by CHARMM version 27 1
> building segment B2
> reading residues from pdb file prot.pdb
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> extracted 271 residues from pdb file
> Info: generating structure...
> unknown residue type HIS
> aliasing residue ILE atom CD1 to CD
> reading coordinates from pdb file prot.pdb for segment B2
> Warning: failed to set coordinate for atom N GLY:1 B2
> [... these warnings go on for a while ...]
> Info: writing psf file nice.psf
> Info: writing pdb file nice.pdb
>
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> ERROR: failed on guessing coordinates
> ERROR: failed on writing structure to psf file
> ERROR: failed on writing coordinates to pdb file
>

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