From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jun 16 2010 - 11:52:23 CDT

Hi Harold,
It would be helpful if you could send me a compressed copy of your
solv.pdb file generated as input to solvate.

By the way, the idiom
[atomselect top all] do something
creates a memory leak and should not be used. Atom selections persist
until explicitly freed; there is no built in facility for proper use of
anonymous atom selections.

Best,
Peter

On 06/16/2010 11:42 AM, Harold Hatch wrote:
>
> 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
>