VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Sat Dec 03 2022 - 05:19:10 CST

W dniu 2.12.2022 o 23:23, Huang, Caleb pisze:
> Hello,
>
> I am trying to create a single amino acid (phosphoserine) using psfgen
> but am having trouble getting coordinates -- I get a pdb file with the
> correct atoms but all zeros. The following is what I tried. Any help
> would be appreciated!

For the coordinates to be read from the tmp.pdb file, both the residue
name and the atom names must match those in "RESI SER" definition in the
file top_all36_prot.rtf. You should see in the console a lot of warnings
from psfgen about missing atom coordinates.

You do have some useless aliases regarding ILE and GLY atom names. I
think the proper command is "pdbalias". Using it, you may tell psfgen
the correspondence of atom names in the pdb and topology files, and use
"pdbalias residue" to rename whatever the residue name is in tmp.pdb to
SER. See the psfgen user guide:
https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/ug.pdf

Or, you can look up the proper names in top_all36_prot.rtf and edit the
tmp.pdb names by hand.

Greetings,

Pawel

>
> package require psfgen
> resetpsf
> set PARAMETERS /cow02/parameters
> topology $PARAMETERS/top_all36_prot.rtf
> topology $PARAMETERS/top_all36_na.rtf
> topology $PARAMETERS/toppar_prot_na_all.str
>
> alias atom ILE CD1 CD
> alias atom GLY OXT OT1
>
> set name phos_SER
> segment L1 {
>  residue 1 SER
> }
>
> patch SP2 L1:1
> regenerate angles dihedrals
> coordpdb tmp.pdb L1
>
> guesscoord
> writepdb $name.pdb
> writepsf $name.psf
>
>
> -Caleb 

-- 
--
dr inż. Paweł Kędzierski
tel. +48 71 320 3200
Instytut Materiałów Zaawansowanych
Wydział Chemiczny Politechniki Wrocławskiej