Reg: solvating in a non-standard solvent

From: Akshay Bhatnagar (
Date: Wed Mar 18 2015 - 01:29:20 CDT

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

I have perfectly used the syntax for solvating the cystine amino acid in

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

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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