Re: 0 coordinates for LES atoms in pdb file after solvation

From: arijit_r_at_chem.iitkgp.ernet.in
Date: Thu Jan 25 2007 - 22:11:04 CST

Dear Dhiraj,
     It would be something like this

#!/usr/local/bin/vmd
# join (parts of) protein complex with a membrane

# set echo on for debugging
echo on

# need psfgen module and topology
package require psfgen
topology top_all27_prot_lipid.inp

resetpsf
readpsf prot_solvate_ion.psf ! this is your protein after
coordpdb prot_solvate_ion.pdb ! solvate and adding ion

# reload full structure (do NOT resetpsf!)
mol load psf prot_solvate_ion.psf pdb prot_solvate_ion.pdb

# select and delete waters that overlap protein:
set selwat [atomselect top "resname TIP3"]
set lseglist [lsort -unique [$selwat get segid]]
foreach lseg $lseglist {
   set selover [atomselect top "segid $lseg and within 3.0 of protein"]
   set resover [lsort -unique [$selover get resid]]
   foreach res $resover {
     delatom $lseg $res
   }
}
foreach res { } {delatom $WAT $res}
foreach res { } {delatom $WAT1 $res}
foreach res { } {delatom $WAT2 $res}
foreach res { } {delatom $WAT3 $res}
foreach res { } {delatom $WAT4 $res}
foreach res { } {delatom $WAT5 $res}
foreach res { } {delatom $WAT6 $res}
foreach res { } {delatom $WAT7 $res}
foreach res { } {delatom $WAT8 $res}

multiply 4 seg:62 ! where seg is the segment name
# write full new structure
writepsf new_all.psf
writepdb new_all.pdb

# clean up

# non-interactive script: vmd -dispdev text < combine.tcl > combine.log
quit

*******
this is the tcl script that i would use...

hope this would help

                                arijit

On Thu, 25 Jan 2007, Dhiraj Srivastava wrote:

> Hi arijit
> Do you know any way to generates LES atoms after preparing Structure file
> and solvating it. I was generating these atoms using PSFGen.
>
> Dhiraj
>
>
> On 1/25/07, arijit_r_at_chem.iitkgp.ernet.in <arijit_r_at_chem.iitkgp.ernet.in>
> wrote:
>>
>> Dear Dhiraj,
>> after solvating and adding ion ( if there is ion in your system) then
>> try to generate the LES atoms.
>> arijit
>>
>> On Thu, 25 Jan 2007, Dhiraj Srivastava wrote:
>>
>> > Hi all
>> > I am planning to run LES and for that i prepared my pdb and psf
>> file
>> > by following PSFGen manual. in this pdb file i was getting same
>> coordinates
>> > for LES atoms. for example
>> >
>> > ATOM 7247 HG2 PRO X2002 11.967 50.579 50.090 0.00 1.00
>> P
>> > H
>> > ATOM 7248 HG2 PRO X2002 11.967 50.579 50.090 0.00 2.00
>> P
>> > H
>> > ATOM 7249 HG2 PRO X2002 11.967 50.579 50.090 0.00 3.00
>> P
>> > H
>> > ATOM 7250 HG2 PRO X2002 11.967 50.579 50.090 0.00 4.00
>> P
>> > H
>> > ATOM 7251 HG2 PRO X2002 11.967 50.579 50.090 0.00 5.00
>> P
>> > H
>> > ATOM 7252 HG2 PRO X2002 11.967 50.579 50.090 0.00 6.00
>> P
>> > H
>> > ATOM 7253 HG2 PRO X2002 11.967 50.579 50.090 0.00 7.00
>> P
>> > H
>> > ATOM 7254 HG2 PRO X2002 11.967 50.579 50.090 0.00 8.00
>> P
>> > H
>> > ATOM 7255 HG2 PRO X2002 11.967 50.579 50.090 0.00 9.00
>> P
>> > H
>> > ATOM 7256 HG2 PRO X2002 11.967 50.579 50.090 0.00 10.00
>> P
>> > H
>> >
>> > for one of the atom of the LES segment.
>> >
>> > but after solvating the structure using solvate command, i am getting a
>> pdb
>> > file where all the coordinates of the atoms (LES) except the first one
>> is 0.
>> > for example -
>> >
>> > ATOM 7247 HG2 PRO X2002 11.967 50.579 50.090 1.00 0.00
>> P
>> > H
>> > ATOM 7248 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00
>> P
>> > ATOM 7249 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00
>> P
>> > ATOM 7250 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00
>> P
>> > ATOM 7251 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00
>> P
>> > ATOM 7252 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00
>> P
>> > ATOM 7253 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00
>> P
>> > ATOM 7254 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00
>> P
>> > ATOM 7255 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00
>> P
>> > ATOM 7256 HG2 PRO X2002 0.000 0.000 0.000 -1.00 0.00
>> P
>> >
>> >
>> > This is creating problem when i am trying to minimize the
>> structure. does
>> > anyone know What may be the reason and how to solve this problem. i am
>> using
>> > the following command for solvating my protein.
>> >
>> > Solvate prodh.psf prodh.pdb -t 10 -o prodh_wb
>> >

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