Re: Reg: solvating in a non-standard solvent

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Mar 18 2015 - 09:08:24 CDT

Hi Akshay Bhatnagar,

Another possible source of the error is what the segname is in the psf,
as that is what VMD actually respects. If its only in the pdb, the order
in which VMD reads the files internally means that there won't be a
segname QQQ like VMD expects. Here is my solvate line for using DCLE:

solvate input.psf input.pdb -s DC -minmax [list [list 0 0 6] [list $x $y
[expr {$membranethickness - 6}]]] -o output -spdb DCLEbox.pdb -spsf
DCLEbox.psf -stop top_all36_cgenff.rtf -ws 113.05 -ks "name C1"

-Josh Vermaas

On 3/18/15 6:19 AM, Branko wrote:
> Akshay,
>
> Check did EACH CH2Cl2 molecule in your solvation box have UNIQUE
> residue number....
>
> Branko
>
> On 3/18/2015 7:29 AM, Akshay Bhatnagar wrote:
>> Hello everyone
>>
>> I have to solvate an amino acid in Dichloroethane (dce) instead of water.
>>
>> From the VMD tutorial i have understood the five prerequisites
>> for this
>>
>> (dce.pdb, dce.psf, dce.top, the unique key selection identifier (ks) and
>> the size of box). I have obtained the dce.pdb from gromacs website
>> (converted the .gro file to .pdb) than i have generated the psf file
>> using
>> the charmm topology file for dichloroethane. the segid in dce_psf.pdb is
>> QQQ.
>>
>> I have perfectly used the syntax for solvating the cystine amino acid in
>> dichloroethane:
>>
>> solvate cystine.psf cystine.pdb -spsf dce_psf.psf -spdb dce_psf.pdb -stop
>> top.inp -ks C1 -ws 10 -o cys-dce
>>
>> But it is giving following error:
>>
>> atomselect: cannot parse selection text: segid QQQ and C1 and same
>> residue
>> as (x < -2.444000005722046 or x > 5.374000072479248 or y <
>> 44.7599983215332 or y > 49.08599853515625 or z < 58.62699890136719
>> or z >
>> 62.95100021362305 or within 2.4 of (not segid QQQ))
>>
>> I am not able to understand where i went wrong. C1 is the atom name
>> that is
>> present in each residue of the DCE box. (similar to OH2, as in case of
>> water box)
>> . Please help to correct this error. All the necessary files are also
>> attached.
>>
>> Thank you very much for the time and suggestions in advance
>>
>> With Regards
>> Akshay Bhatnagar
>> PhD Student
>> BITS Pilani Hyderabad Campus
>>
>

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