VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Oct 22 2018 - 12:53:34 CDT

Hi Francesco,

Unless you changed your topology file, the C8 was defined (in your first
email) as "ATOM C8 CG2D1 0.098". I don't know how your corrected patch
looks like but you can change the atom type in the patch, like "ATOM 1C8
 CG321 -0.124 "

Whenever you have to change the atom type of a structure, please do it at
the psfgen level, not changing the psf file.

Best

João

On Mon, Oct 22, 2018 at 12:08 PM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Sorry, (I tried correcting the .psf file by replacing CG2D1 with CG32),
> should be read (I tried correcting the .psf file by replacing CG2D1 with
> CG321).
> f
>
> ---------- Forwarded message ---------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Mon, Oct 22, 2018 at 7:03 PM
> Subject: Re: vmd-l: psfgen patching protein-ligand
> To: <jribeiro_at_ks.uiuc.edu>
> Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
>
> Hi
> Previously I answered OK, while now problems emerge with minimization.
> psfgen assigned atom types to the ligand
> C7 (CG205 carbonyl C)
> C8 (CG2D1 alkene; RHC=; imine C))
> C9 (CG314 aliphatic C with 1H, adjacent to N+)
>
> O H H
> || | |
> C7-C8-C9-C10
> |
> H
>
> C9 assignment is correct, as this is for bond with HSP NE2, following the
> patching indications.
> C7 assignment is also correct.
>
> C8 assignment is making wrong chemistry, it should be CG321, while the
> .str param file for the ligand reads accordingly
> ATOM C8 CG321 -0.124 ! 2.500
>
> Therefore, minimization crashes with error: no bond parameters for CG2D1
> CG205
>
> What to do? I can not assume any bug in psfgen. I tried correcting the
> .psf file by replacing CG2D1 with CG32, which raised other major problems--0000000000005367f00578d4efed--