Re: Fwd: phosphotyrosine

From: poker_at_physics.usyd.edu.au
Date: Mon Jun 20 2011 - 01:42:49 CDT

A patch statement should work. Name your residue to the base TYR, and
when you make the psf file, load in the CHARMM stream file in addition
to the standard topology file, then add a patch statement similar to
the following:
patch TP2 P1:62
.assuming the residue is in segment P1, with resid 62
ATOM 570 N TYR K 62 -6.070 20.852 19.282 1.00 0.00 P1

- Poker.

Quoting bharat gupta <bharat.85.monu_at_gmail.com>:

> ---------- Forwarded message ----------
> From: bharat gupta <bharat.85.monu_at_gmail.com>
> Date: Mon, Jun 20, 2011 at 9:26 AM
> Subject: Re: phosphotyrosine
> To: namd-l_at_ks.uiuc.edu
>
>
> Hi,
>
> I have a docked complex of my protein with phosphotyrosine, Now I want to
> carry out simulation with that in order to predict the binding affinity. I
> have found out that CHARMM FF has some patch for PTYR, but I don't know how
> to use it ??... can anybody help me
>
> --
> Bharat
>
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
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>

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