VMD-L Mailing List

From: Huang, Caleb (cjhuang_at_UTMB.EDU)
Date: Fri Dec 02 2022 - 16:23:54 CST

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!

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