From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Thu Mar 19 2015 - 11:59:28 CDT
In addition to Jeff's comment: make sure you use correct names with primes, i.e. maybe you need "name C1'" ?
> On Mar 19, 2015, at 9:02 AM, 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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