From: Muhittin Emre Özdemir (muhittinozdemir_at_gmail.com)
Date: Tue May 09 2006 - 04:06:46 CDT
Hi everyone,
I am rying to simulate a protein with heme. I am able to create all the
files necessary for simulation. but I noticed something odd in the
simulation I made. There should be a link between a S atom of cysteine and
Fe atom of heme, which is why i am asking help for. The link doesn't exist.
I guess there is something wrong with the final pdb and psf files. This is
the script I use for creating them:
package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
pdbalias residue HEM HEME
segment C {pdb cyp1.pdb}
segment H {pdb hem1.pdb}
coordpdb cyp1.pdb C
coordpdb hem1.pdb H
guesscoord
writepdb cyp2.pdb
writepsf cyp2.psf
Any ideas?
Thanks in advance for your help...
-- Muhittin Emre Özdemir
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