regarding editing protonated glutamate in the pdb file via psfgen

From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Tue Nov 05 2013 - 00:53:17 CST

Dear NAMD-Experts, I need an assistance regarding editing a pdb file containing a protonated Glutamate. I am pasting below the description of Glutamate (Glu) and protonated Glutamate (GluP) given in topology.  GLUTAMATE  RESI GLU         -1.00 GROUP ATOM N    NH1    -0.47  !     | ATOM HN   H       0.31  !  HN-N ATOM CA   CT1     0.07  !     |   HB1 HG1   OE1 ATOM HA   HB      0.09  !     |   |   |    // GROUP                   !  HA-CA--CB--CG--CD ATOM CB   CT2    -0.18  !     |   |   |    \ ATOM HB1  HA      0.09  !     |   HB2 HG2   OE2(-) ATOM HB2  HA      0.09  !   O=C GROUP                   !     | ATOM CG   CT2    -0.28 ATOM HG1  HA      0.09 ATOM HG2  HA      0.09 ATOM CD   CC      0.62 ATOM OE1  OC     -0.76 ATOM OE2  OC     -0.76 ............................. .............................. ........... PROTONATED GLUTAMATE PRES GLUP         0.00 ! patch for protonated glutamic acid, proton on oe2 GROUP                  ! via acetic acid, use in a patch statement and                        ! follow with AUTOgenerate ANGLes DIHEdrals command ATOM CG   CT2    -0.21 ! ATOM HG1  HA      0.09 ! HG1    OE1 ATOM HG2  HA      0.09 !  |    // ATOM CD   CD      0.75 ! -CG--CD ATOM OE1  OB     -0.55 !  |     \ ATOM OE2  OH1    -0.61 ! HG2     OE2-HE2 ATOM HE2  H       0.44 ! BOND OE2 HE2 DONOR HE2 OE2 .............................. ............................. ... In my pdb, Glu 173 is protonated.  So, while editing for creating psf and pdb files; I included the following line :  set G173 [atomselect top "resname GLU and resid 173"] $G173 set resname GLUP But, the psfgen is not recognizing the resname GLUP (inspite of the toplogies of Protonated Glutamate are given).   So, I don't know how to edit this particular protonated Glutamate and make psfgen work for creating the pdb and psf. Any assistance regarding this will be greatly appreciated. Thanking You, Prathit

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