VMD-L Mailing List

From: OZGE ENGIN (OZENGIN_at_KU.EDU.TR)
Date: Sat Nov 08 2008 - 03:17:41 CST

Hi all,

Hi All,

I have a problem on the usage of patch for adding diphosphate group to uracil nucleoside. In the Charmm sugar file, this patch is indicated as 5DP. I have already the uracil nucleoside (N-base+ribose sugar). I could not find any information for the usage of this patch (5DP).

Could you give some information for the usage of this patch?

Thanks in advance

-----Original Message-----
From: "OZGE ENGIN" <OZENGIN_at_KU.EDU.TR>
To: vmd-l_at_ks.uiuc.edu
Date: Fri, 29 Feb 2008 21:30:01 +0200
Subject: vmd-l: unusual bond between the cysteine and arginine residue during the simulation

Hi all,

I perform a simulation of a 24-residue peptide at air/water interface. While I am looking at the trajectory, I see that there is an unusual bond (long bond) between the cysteine and arginine residue. However, I have another cysteine residue but it does not make any bond with any other residue.Both residues are charged.

What may be the reason?
Ozge Engin
=================================
Computational Science & Engineering
Koc University

Ozge Engin
=================================
Computational Science & Engineering
Koc University