Re: patch

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Mar 31 2017 - 07:49:16 CDT

A good starting point would be the documentation of the "patch" command in
the psfgen user's guide.

Giacomo

On Fri, Mar 31, 2017 at 5:03 AM, <hem_chandra_at_iitg.ernet.in> wrote:

>
>
> Hello Namd,
>
> 1. top_all36_rtf contains a residue defined as PRES CT1. I want to patch
> this to the last residue of my protein.
>
> 2. another molecule BOC (whose cgenff generated str file is attached
> herewith), which I want to patch it to the first residue of the peptide
> chain.
> https://drive.google.com/open?id=0B77lRAKVhq_RZjJXQ0haZlhhRjg
> https://drive.google.com/open?id=0B77lRAKVhq_RWWlkTE0zajRTY00
>
> please suggest me how I should do it using NAMD.
>
> Thanking in anticipation
> _hem
>
>
>
> ps:
>
>
> ### this is just a concerened part from top_all36_prot.rtf
>
>
> PRES CT1 0.00 ! methylated C-terminus from methyl acetate
> GROUP ! use in generate statement
> ATOM N NH1 -0.47 ! don't use with Gly or Pro
> ATOM HN H 0.31 ! OT1
> ATOM CA CT1 0.17 ! | //
> ATOM HA HB1 0.09 ! -N--CA--C HT1
> ATOM C CD 0.63 ! | | \ /
> ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2
> ATOM OT2 OS -0.34 ! \
> ATOM CT CT3 -0.14 ! HT3
> ATOM HT1 HA3 0.09 !
> ATOM HT2 HA3 0.09 !
> ATOM HT3 HA3 0.09 !
> DELETE ATOM O
> BOND C OT2 OT2 CT
> BOND CT HT1 CT HT2 CT HT3
> DOUBLE C OT1
> IMPR C CA OT2 OT1
> ACCEPTOR OT1 C
> ACCEPTOR OT2 C
> IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
> IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
> IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000
> IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000
> IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000
> IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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