From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Thu Mar 19 2015 - 23:38:24 CDT
Yes sir, I included "name" in -ks, but it gave the same error.
With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus
On Thu, Mar 19, 2015 at 7:32 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> Not including "name" in -ks was the problem causing the error. If it
> is still not working, do you receive a different error?
>
> 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 Thu, Mar 19, 2015 at 1:40 AM, Akshay Bhatnagar
> <akshaybhatnagar2790_at_gmail.com> wrote:
> > 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
> >> >
> >
> >
>
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:01 CST