Re: Reg: solvating in a non-standard solvent

From: Jeff Comer (
Date: Wed Mar 18 2015 - 09:44:12 CDT


I think I see the problem. If you look in the selection text, it says
"...and C1 and..." This is what you've given for -ks, but it's not
valid selection text.

You want -ks "name C1", probably.


Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311

On Wed, Mar 18, 2015 at 1:29 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,, 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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