From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Wed Mar 18 2015 - 07:19:45 CDT
Akshay,
Check did EACH CH2Cl2 molecule in your solvation box have UNIQUE residue
number....
Branko
On 3/18/2015 7:29 AM, Akshay Bhatnagar 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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