Tutorial-l Mailing List

From: Sridhar Kumar Kannam (srisriphy_at_gmail.com)
Date: Wed Aug 13 2014 - 00:58:50 CDT

Dear NAMD users,

I have followed the tutorial "*Residue-Based Coarse-Graining" *carefully
and applied similar steps (as for the Ubiquitin example given) to build a
coarse-grained model for BSA (pdb id: 3V03).

Everything went OK in building the cg model, but when I run the simulation
I got the following error:
UNABLE TO FIND BOND PARAMETERS FOR N0H P4 (ATOMS 126 128)

Atom 128 corresponds to the (single) bead of Alanine.
Alanine bead should have one of these BAS names only - BAS = P4C, P4B, P4F,
C5H, N0H, N0T or N0E. But my coarse-grained protein psf file has the name
P4 as the error says.

While building the correct cg psf file using 02b-correct-CG-psf.tcl, the
log file says
Secondary structure is H. Applying patch ACI A:128 to segname A resid 128.

But this is not written in the psf file. So there is some problem in
applying the patch.

A very similar problem was asked in the mailing list before but unanswered
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/21292.html

Any ideas on solving the problem ...

Thank you very much. 

-- 
Cheers !!!
Sridhar  Kumar Kannam :)
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