From: Jinasena Hewage (jwhewage_at_gmail.com)
Date: Fri Jul 03 2015 - 15:03:41 CDT

Thank you very much Zoran. I completely forgot the case.
Thank you
Hewage

On Fri, Jul 3, 2015 at 3:56 PM, zoran <zmatovic_at_kg.ac.rs> wrote:

> Hi Hewage,
>
>
> I am trying to generate the psf file, and add ACE and CT3 groups to
> terminals of my peptide chain. I have been using the following script.
>
> package require psfgen
> psfcontext reset
> topology top_all22_prot_cmap.inp
> segment mgn {
> pdb helix1.pdb
> first ACE
> last CT3
> }
> coordpdb helix1.pdb mgn
> guesscoord
> regenerate angles dihedrals
> writepdb mgn1_new.pdb
> writepsf mgn1_new.psf
> quit
>
> But for this case it give me an error message saying,
>
> ...............
> psfgen) cross-term entries present in topology definitions
> psfgen) building segment MGN
> psfgen) reading residues from pdb file helix1.pdb
> psfgen) unknown residue type HIS
> psfgen) extracted 15 residues from pdb file
> psfgen) setting patch for first residue to ACE
> psfgen) setting patch for last residue to CT3
> psfgen) Info: generating structure...psfgen) unknown residue type HIS
> failed!
> ERROR: failed on end of segment
> ...................
>
>
> You should according to the namd tutorial do next after topologu hes been
> communicated:
>
> pdbalias residue HIS HSE pdbalias atom ILE CD1 CD
>
> Tutorials said:
> 1. Change the residue name of histidine to the proper name found in the
> topology file. HSE is one of three names for histidine, based on the
> protonation state of its side group.
> 2. The atom named ``CD1" ([image: $\delta$] carbon) in isoleucine
> residues is renamed as ``CD", its proper name from the topology file. Since
> isoleucine contains only one [image: $\delta$] carbon atom, the psf file
> does not use the number label after ``CD".
>
> Hope this help
> Zoran
>
>
>
> Can some one please help me.
> Thank you
> Hewage
>
>
>
>
> --
> Dr. Jinasena Hewage
> Senior Lecturer in Physical Chemistry
> (Current Position: Visiting Academic, Research School of Chemistry,
> Australian National University)
> Department of Chemistry
> University of Ruhuna
> Matara, Sri Lanka
> (+94) 071 4500 389
>

-- 
Dr. Jinasena Hewage
Senior Lecturer  in Physical Chemistry
(Current Position: Visiting Academic, Research School of Chemistry,
Australian National University)
Department of Chemistry
University of Ruhuna
Matara, Sri Lanka
(+94) 071 4500 389