From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Fri Jul 25 2014 - 12:20:46 CDT
Sadegh,
It looks like you've been ignoring most of my suggestions so far. I'm
going to assume this is a communication barrier and show you what I mean
by attaching the correct solution. With this and my e-mail of yesterday,
there should be enough examples available to make it crystal-clear how to
construct simple 2-residue patches, so the next person asking how to link
two side chains together will be referred to these two posts and will have
to learn by doing.
Kenno.
PS. To repeat yesterday's reminder, most of the patches in the CHARMM
force field should be followed by generation of angles and dihedrals from
the bond list, and this one is no exception. The command to do so in
CHARMM is "AUTOgenerate ANGLes DIHEdrals"; the psfgen equivalent should be
"auto angles dihedrals" or "regenerate angles dihedrals" or something like
that (I don't know the exact syntax).
On 07/22/2014 06:04 AM, Sadegh Faramarzi Ganjabad wrote:
> Kenno
>
> Following is the patch;
>
> PRES LINK 0.00 ! linkage for IMAGES or for joining segments
> ! 1 refers to previous (N terminal) -->
> Asp3
> ! 2 refers to next (C terminal) --> Lys10
> ! use in a patch statement
> ! follow with AUTOgenerate ANGLes
> DIHEdrals command
> ! used to link Asp3 to Lys10 in shu-9119
> !
> ! 1HB1 1HB2
> ! \ /
> ! --1CB
> ! \
> ! 1CG==OD1
> ! \
> ! 2NZ- 2HZ1
> ! |
> ! 2HE2 - 2CE- 2HE1
> ! |
>
> DELETE ATOM 1OD2
> DELETE ATOM 2HZ2
> DELETE ATOM 2HZ3
> !GROUP
> !ATOM CB CT2A -0.27
> !ATOM HB1 HA2 0.10
> !ATOM HB2 HA2 0.10
> !ATOM CG CC 0.63
> !ATOM OD1 OC -0.75
> !ATOM CE CT2 0.22
> !ATOM HE1 HA2 0.06
> !ATOM HE2 HA2 0.06
> !ATOM NZ NH3 -0.29
> !ATOM HZ1 HC 0.34
> BOND 1CG 2NZ
>
> Sadegh
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