VMD-L Mailing List
From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Oct 16 2018 - 10:21:24 CDT
- Next message: Francesco Pietra: "Re: psfgen patching protein-ligand"
- Previous message: Francesco Pietra: "psfgen patching protein-ligand"
- In reply to: Francesco Pietra: "psfgen patching protein-ligand"
- Next in thread: Francesco Pietra: "Re: psfgen patching protein-ligand"
- Reply: Francesco Pietra: "Re: psfgen patching protein-ligand"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: Francesco Pietra: "Re: psfgen patching protein-ligand"
- Previous message: Francesco Pietra: "psfgen patching protein-ligand"
- In reply to: Francesco Pietra: "psfgen patching protein-ligand"
- Next in thread: Francesco Pietra: "Re: psfgen patching protein-ligand"
- Reply: Francesco Pietra: "Re: psfgen patching protein-ligand"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]