From: Mohammad Hassan Khatami (mhk302_at_mun.ca)
Date: Mon Jul 24 2017 - 13:29:18 CDT
Hi,
I am new to NAMD, and I am planning to simulate a glucose chain of AGLC
residues, using CHARMM36 in NAMD. In my structures AGLCs are connected
through 1->4 connections represented below:
AGLC--1->4--AGLC--1->4--AGLC--1->4--AGLC--1->4--AGLC
In the "top_all36_carb.rtf" file I was able to find AGLC parameters for
stand-alone residue and "PRES 14aa" and "PRES 14ab" sections, which I
assume they should be responsible for the 1->4 connections of AGLC. My
question is that if I have to add the command similar to:
Patch 14aa .... .....
into my .pgn file, or is it also correct to modify the
"top_all36_carb.rtf" file and introduce modified residues of AGLC
manually based on the position of AGLC in the chain, like below:
FIRST--1->4--MIDDLE--1->4--MIDDLE--1->4--MIDDLE--1->4--LAST.
So I would have residues FIRST, MIDDLE and LAST into "top_all36_carb.rtf".
Best,
Mohammad
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