Re: Reg: solvating in a non-standard solvent

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Thu Mar 19 2015 - 12:06:38 CDT

I've looked at your molecule's topology and it looks like you don't need any primes.

> On Mar 19, 2015, at 11:59 AM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>
> 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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