From: ravi sharma (rdsharma_4u_at_yahoo.com)
Date: Mon Apr 16 2007 - 14:11:47 CDT
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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