From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Thu Mar 19 2015 - 01:40:55 CDT
Hello
Thank you very much for taking time answer but, all the molecules have
unique residue numbers. the segname in psf is QQQ. And also, when i tried
using [-ks "name C1"], has also not worked.
With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus
On Wed, Mar 18, 2015 at 8:14 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> Hi,
>
> 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.
>
> Jeff
>
> –––––––––––––––––––––––––––––––––––———————
> 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
> <akshaybhatnagar2790_at_gmail.com> 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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