VMD-L Mailing List

From: Harold Hatch (hhatch_at_princeton.edu)
Date: Wed Jun 16 2010 - 10:42:50 CDT

Dear VMD users and developers,

 

I am having trouble solvating a protein with a nonstandard solvent using the
solvate package.

 

The protein is ubiquitin, the solvent of choice is water/trehalose mixture.
The vmd script is shown below, and goes as follows: build trehalose, build
ubiquitin, solvate ubiquitin with trehalose, solvate both with water. But
when I attempt to solvate ubiquitin with trehalose, I receive the following
error:

 

no segment QQQ

Segment QQQ not exsisting, skipping patch 11AA.

 

Which results in a psf/pdb of a protein surrounded by several 'sugars'
without the proper alpha-alpha linkage patch on the two glucose molecules to
form trehalose. The atoms which should have been eliminated in the
'dehydration reaction' to form trehalose from two glucose (HO1 on residue 1,
HO1 and O1 on residue 2) are printed in the final pdb, with coordinates of
{0.0 0.0 0.0}.

 

An example of the final PDB (ubqti_wb.pdb) is shown below, followed by the
entire vmd script that I used to generate it. Please let me know what other
useful information I have neglected to share with you.

 

Thank you,

Harold

 

*********EXAMPLE OF PDB************

.

ATOM 1230 HA1 GLY U 76 9.240 10.892 18.107 1.00 0.00 U
H

ATOM 1231 HA2 GLY U 76 10.900 11.564 18.409 1.00 0.00 U
H

ATOM 1232 C1 AGLCW 1 -7.954 17.235 -8.710 1.00 0.00 W30
C

ATOM 1233 H1 AGLCW 1 -8.167 18.087 -8.015 1.00 0.00 W30
H

ATOM 1234 O1 AGLCW 1 -8.316 15.956 -8.278 1.00 0.00 W30
O

ATOM 1235 HO1 AGLCW 1 0.000 0.000 0.000 -1.00 0.00 W30
H

ATOM 1236 C5 AGLCW 1 -6.128 16.467 -10.162 1.00 0.00 W30
C

.

 

*************** VMD SCRIPT *************************

#vmd script to build ubiquitin solvated in trehalose + water

resetpsf

package require psfgen

topology top_all22_prot_carb.rtf

 

#build trehalose for solvate package

pdbalias residue TRE AGLC

segment QQQ {pdb trehalose.pdb}

patch 11AA QQQ:1 QQQ:2

regenerate angles dihedrals

coordpdb trehalose.pdb QQQ

guesscoord

writepdb solv.pdb

writepsf solv.psf

 

#center trehalose

mol new solv.psf

mol addfile solv.pdb

set everyone [atomselect top all]

[atomselect top all] moveby [vecmul {-1 -1 -1} [measure center $everyone]]

[atomselect top all] writepdb solv.pdb

 

#build ubiquitin

resetpsf

pdbalias residue HIS HSE

pdbalias atom ILE CD1 CD

segment U {pdb ubqp.pdb}

coordpdb ubqp.pdb U

guesscoord

writepdb ubqti.pdb

writepsf ubqti.psf

 

#center prot

mol new ubqti.psf

mol addfile ubqti.pdb

set everyone [atomselect top all]

[atomselect top all] moveby [vecmul {-1 -1 -1} [measure center $everyone]]

[atomselect top all] writepdb ubqti_center.pdb

 

#solvate prot

package require solvate

solvate ubqti.psf ubqti_center.pdb -spdb solv.pdb -spsf solv.psf -stop
top_all22_prot_carb.rtf -ks "name C1" -ws 12 -minmax {{-20 -20 -20} {20 20
20}} -s W -o ubqti_wb