From: Marc Charendoff (mcharend_at_sbcglobal.net)
Date: Thu Mar 10 2011 - 19:07:33 CST
Hello,
I have attempted to use the autopsf package to create a topology for
an N-terminus ACE cap on a proline residue. The initial pdb looked a bit strange
in VMD which I thought might be an artifact that would resolve after
minimization. However, after 2000 steps of minimization, I still see a strange
topology rendered for the ACE-PRO structure in VMD. I have listed my pdb
and psf file portions below. My minimization was done
using par_all27_prot_na.prm.
Thanks, Marc
PDB
REMARK original generated coordinate pdb file
ATOM 1 CAY ACE X 1 -15.305 1.914 0.532 1.00 0.00 P1 C
ATOM 2 HY1 ACE X 1 -15.847 1.726 -0.287 1.00 0.00 P1 H
ATOM 3 HY2 ACE X 1 -15.007 2.869 0.532 1.00 0.00 P1 H
ATOM 4 HY3 ACE X 1 -15.847 1.726 1.351 1.00 0.00 P1 H
ATOM 5 CY ACE X 1 -14.499 1.322 0.532 1.00 0.00 P1 C
ATOM 6 OY ACE X 1 -13.957 1.510 1.351 1.00 0.00 P1 O
ATOM 7 N PRO X 1 -14.517 0.748 -0.287 1.00 0.00 P1 N
ATOM 8 CD PRO X 1 -15.632 0.187 -1.322 1.00 0.00 P1 C
ATOM 9 HD1 PRO X 1 -16.083 -0.808 -1.100 1.00 0.00 P1 H
ATOM 10 HD2 PRO X 1 -16.454 0.937 -1.393 1.00 0.00 P1 H
ATOM 11 CA PRO X 1 -13.346 -0.113 -0.287 1.00 0.00 P1 C
PSF
8 !NTITLE
REMARKS original generated structure x-plor psf file
REMARKS 2 patches were applied to the molecule.
REMARKS topology Peptide8_1_autopsf-temp.top
REMARKS topology /Applications/VMD
1.8.6.app/Contents/vmd/plugins/noarch/tcl/solvate1.2/wat.top
REMARKS segment P1 { first ACE; last CT2; auto angles dihedrals }
REMARKS segment WT1 { first NONE; last NONE; auto none }
REMARKS patch ACE P1:1
REMARKS patch CT2 P1:8
9023 !NATOM
1 P1 1 ACE CAY CT3 -0.270000 12.0110 0
2 P1 1 ACE HY1 HA 0.090000 1.0080 0
3 P1 1 ACE HY2 HA 0.090000 1.0080 0
4 P1 1 ACE HY3 HA 0.090000 1.0080 0
5 P1 1 ACE CY C 0.510000 12.0110 0
6 P1 1 ACE OY O -0.510000 15.9990 0
7 P1 1 PRO N N -0.290000 14.0070 0
8 P1 1 PRO CD CP3 0.000000 12.0110 0
9 P1 1 PRO HD1 HA 0.090000 1.0080 0
10 P1 1 PRO HD2 HA 0.090000 1.0080 0
11 P1 1 PRO CA CP1 0.020000 12.0110 0
12 P1 1 PRO HA HB 0.090000 1.0080 0
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