Re: How to make alkaline ph pgn file

From: Gaurav Sharma (
Date: Mon Apr 16 2007 - 21:59:26 CDT


I don't remember seeing the 'LSN' form of Lysine in any molecular
modeling study. Where did you find it?

I guess by 'alkaline pH' you mean pH~11 or higher. I am not sure if NAMD
force-field in its present form can support this . Your best bet would
be develop your own force-field for lysine using QM simulations.


ravi sharma wrote:

> Hello Sir,
> its Ravi have seen your mail namd website ,,,sir i got a problem that
> i am doing simualtion (MD)at different ph ......
> at Neutral ph,Histidine exist in the form of HSE and at the acidic ph
> it exist in HSD form that also i found at topology file.....completed
> my simulation successfully
> But now i got the problem that in alkaline ph LYSINE exist at LSN form
> but i didnt get it in toplogy file so simulation will not run if i
> patched it....
> Like acidic ph pgn as..........
> package require psfgen
> topology top_all27_prot_lipid.inp
> pdbalias atom ILE CD1 CD
> pdbalias residue HIS HSP
> pdbalias residue HEM HEME
> segment U {pdb A.pdb}
> coordpdb A.pdb U
> segment H {pdb heme.pdb}
> coordpdb heme.pdb H
> patch ASPP U:17
> patch ASPP U:28
> patch ASPP U:35
> patch ASPP U:36
> patch ASPP U:94
> patch GLUP U:4
> patch GLUP U:9
> patch GLUP U:13
> patch GLUP U:39
> patch GLUP U:60
> patch GLUP U:61
> .........please can you help me to generate pgn for alkaline ph
> Thanx
> Best Regards
> Looking for your postive response
> Ravi Datta Sharma
> Department of Microbiology
> CCS Unversity,
> Meerut
> "A friend in
> Need is a friend's indeed."
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> <*>

Gaurav Sharma
Computational BioNano Robotics Lab
Northeastern University
Boston, MA - 02115
Tel: 617-373-2970 

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