From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Thu Mar 19 2015 - 09:02:10 CDT
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
>> >
>
>
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