VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Sep 18 2006 - 09:45:03 CDT

Hi Daniel,

For such purpose you can use psfgen as follows:

topology toppar/top_all27_prot_na.rtf
topology toppar/stream/toppar_prot_na_all.str
alias atom ILE CD1 CD
alias atom GLY OXT OT1
segment RLCP { pdb rlc-opt.pdb
}
patch SP2 RLCP:125
regenerate angles dihedrals
coordpdb rlc-opt.pdb RLCP
guesscoord
writepdb rlc-hc-p.pdb
writepsf rlc-hc-p.psf

You will need the topology files for the protein
(top_all27_prot_na.rtf) and the stream file for the P-Ser
(topppar_prot_na_all.str). Please note that I'm applying the SP2
patch, which is the P-Ser with a net charge of -2.

If you have questions about it, please let me know.

Good luck!
Michel

2006/9/18, Dani Süveges <suvi.dani_at_gmail.com>:
> Hi!
>
> I'm planning to simulate the effect of a phosphorylation on a serin
> residue of a known structure. But I don't know how to insert the
> phosphate group into the .pdb file. Is there option included in VMD or
> should I use an other program? (It seems rather difficult to calculate
> the coordinates on my own)
>
>
> thank you!
>
>
> daniel
>