VMD-L Mailing List

From: sseefeld_at_uwm.edu
Date: Fri Aug 25 2006 - 00:33:10 CDT

In making my 2YCC Cytochrome C protein I was encountering issues with
minimization. I have since isolated this issue to the heme segement. I did this
by mimimizing the protein w/o the heme in waterbox, and the heme by itself in
waterbox. The protein w/o the heme gave me no problems and start giving me data
so I eliminated the possibility of it causing the problems. The heme
minimization however gives me "FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND
CPM - HB IN PARAMETER FILES". This leads me to believe that i am constructing
the psf/pdb files incorrectly. If anyone could take a look at the scripts I am
using and see what i am doing wrong please let me know.

Here are the scripts i used. This is using 2YCC off the pdb databank.

1st
## Script to separate 2YCC.pdb into 3 parts
mol load pdb 2YCC.pdb

set heme [atomselect top heme]

$heme writepdb 2YCCheme.pdb

set protein [atomselect top protein]

$protein writepdb 2YCCprotein.pdb

set water [atomselect top water]

$water writepdb 2YCCwater.pdb

2nd
##script to put protein segment into waterbox
mol load pdb 2YCCprotein.pdb

package require psfgen

topology top_all27_prot_lipid_ycc.inp

pdbalias residue HEM HEMO

pdbalias residue HOH TP3M

segment B {pdb 2YCCprotein.pdb

mutate 72 TML}

coordpdb $name.pdb B

guesscoord

writepdb 2YCCproteintml.pdb

writepsf 2YCCproteintml.psf

package require solvate

solvate 2YCCproteintml.psf 2YCCproteintml.pdb -t 12 -o 2YCCproteintml_wb

3rd
##script to put heme in waterbox

mol load pdb 2YCCheme.pdb

package require psfgen

topology top_all27_prot_lipid_ycc.inp

pdbalias residue HEM HEMO

segment B {pdb 2YCCheme.pdb}

coordpdb 2YCCheme.pdb B

guesscoord

writepdb 2YCCheme1.pdb

writepsf 2YCCheme1.psf

package require solvate

solvate 2YCCheme1.psf 2YCCheme1.pdb -t 12 -o 2YCCheme1_wb

Then I just run a generic NAMD run to test if things will work out.

I can send anyone the par/top files if they want as well I just didn't want to
send both of them over the mailing list to everyone. Any help in this will be
greatly appreciated.

Thanks in advance,
Sean Seefeld 

-- 
Sean Seefeld
Undergraduate Researcher
University of Wisconsin - Milwaukee
3210 N. Cramer Street
Milwaukee, WI 53211-3029
sseefeld_at_uwm.edu