From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Wed Mar 25 2015 - 02:38:00 CDT
I found that the problem was with the segid conflict between psf and pdb of
solvent. but when i tried solvation this time, i have observed that with
solvation command i have used it is giving a structure with all the atoms
in the box, so actually during istead of solvation it is just combining the
amino acid structure and the dichloroethane structure, it is giving a
waring output like this:
"truncating segid WTBHN to 4 characters allowed by pdb format", in every
line WTBHN changes to WTBH*O*, *WTBH**P**,*WTBH*Q. *
*can anyone please let me know how to solvate the amino acid in the DCE
solvent instead of just joining them (solvation should remove some DCE
atoms and the box size should be according to the input size)*
*If i am not able to explain the problem, please let me know, i will try to
explain it again in a better way.*
*Thank you very much *
With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus
On Fri, Mar 20, 2015 at 10:08 AM, Akshay Bhatnagar <
akshaybhatnagar2790_at_gmail.com> wrote:
> 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
>> >> >
>> >
>> >
>>
>
>
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