VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Oct 16 2018 - 10:47:35 CDT

Hi Joao
Thanks a lot for correcting my PRES. Now no warning in the log file about
either patching or improper setting, however, neither atom H91 at the
methylene carbon of the ligand, nor HE2 of HSP were removed, and the
intended bond was not formed.

Correction to my PRES reads
.........
DELETE ATOM H91
DELETE ATOM HE2
BOND C9 NE2
! IMPR NR3 CPH1 CPH2 CG314
! IMPR NR3 CPH2 CPH1 CG314
IMPR NE2 CD2 CE1 C9
IMPR NE2 CE1 CD2 C9

Since a long time I had no need of patching. It seems that I forgot the
rules.
Thanks for advice

francesco

On Tue, Oct 16, 2018 at 5:21 PM João Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> Hi Francesco,
>
> The definition of your improper angles should be done using atoms' name
> (e.g NE2) and not type (e.g. NE3).
>
> Best
>
> João
>
> On Tue, Oct 16, 2018 at 10:13 AM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> Hi
>> I can't understand the error message in trying to bind the sp3 carbon C9
>> of a ligand to the NE2 atom of HSP residue, which implies deleting the HE2
>> atom of HSP and the H91 atom at C9 of the ligand.
>>
>> PRES ZAHI 0.661 ! patch for ligand to HSP bonding
>>> ! use in patch statement
>>> ! follow with AUTOgenerate ANGles DIHEdrals command
>>> GROUP !
>>> ATOM C10 CG311 0.303 !
>>> ATOM C9 CG314 0.17 !
>>> ATOM H91 HGA1 0.09 !
>>> ATOM C8 CG2D1 0.098 ! CD2--NE2--CE1
>>> GROUP ! /
>>> ATOM CD2 CPH1 0.19 ! C10--C9--C8
>>> ATOM NE2 NR3 -0.51 ! |
>>> ATOM CE1 CPH2 0.32 ! H91
>>> DELETE ATOM H91
>>> DELETE ATOM HE2
>>> BOND C9 NE2
>>> IMPR NR3 CPH1 CPH2 CG314
>>> IMPR NR3 CPH2 CPH1 CG314
>>>
>>
>> the error message reads
>>
>> psfgen) no atom NR3 in residue HSP:227 of segment PROD
>>
>> and therefore patching failed, while the .psf file shows that NE2 of HSP
>> is a NR3 type atom.
>>
>> My PRES should be wrongly set. Thanks for advice.
>>
>> francesco pietra
>>
>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> http://www.ks.uiuc.edu/~jribeiro/
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>