How to make alkaline ph pgn file

From: ravi sharma (
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
 Best Regards
 Looking for your postive response

  Ravi Datta Sharma
  Department of Microbiology
  CCS Unversity,
                                                           "A friend in Need is a friend's indeed."

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