From: shyamala (
Date: Thu Jul 12 2007 - 13:02:04 CDT

Hi all,

I am fairly new to VMD and NAMD. I am trying to immerse a protein dimer in a box of water.

I am using the following script to accomplish the task.

package require psfgen
package require solvate

# X-PLOR topology files
topology ./topallhdg.inp
topology ./toptip3p.inp

pdbalias atom ILE CD1 CD
pdbalias residue HOH TIP3
pdbalias atom HOH O OH2

set prot "1hbv"
mol load pdb ${prot}.pdb

set all [atomselect top "all"]
set hivp [atomselect top "protein"]

set chainA [atomselect top "chain A"]
set chainB [atomselect top "chain B"]
set xtalH2O [atomselect top "water and resid 501"]
set ligand [atomselect top "resname GAN"]

$chainA writepdb ${prot}_A.pdb
$chainB writepdb ${prot}_B.pdb
$xtalH2O writepdb ${prot}_H2O.pdb
$ligand writepdb ${prot}_lig.pdb


segment A {
first PROP
pdb ${prot}_A.pdb
coordpdb ${prot}_A.pdb A

segment B {
first PROP
pdb ${prot}_B.pdb
coordpdb ${prot}_B.pdb B

segment H {pdb ${prot}_H2O.pdb}
coordpdb ${prot}_H2O.pdb H


writepdb ${prot}_dry.pdb
writepsf x-plor ${prot}_dry.psf

solvate ${prot}_dry.psf ${prot}_dry.pdb -t 5 -o ${prot}_wb

set all [atomselect top "all"]

echo "Min and max box coordinates:"
measure minmax $all
echo "Center of box:"
measure center $all


when I run the script in vmd, I get the following error:
building segment A
setting patch for first residue to PROP
reading residues from pdb file 1hbv_A.pdb
extracted 99 residues from pdb file
Info: generating structure...
unknown atom type +CA
add atom failed in patch PROP
ERROR: failed on end of segment

I am not really sure what this means. Both chains A and B of the protein dimer have a N term Proline (residue 1). I am using xplor topology files.

I would really appreciate it if someone could give some ideas about what is going wrong.


Shyamala Iyer
University of Washington, Seattle