From: Irene Newhouse (einew_at_hotmail.com)
Date: Wed Apr 06 2011 - 14:02:30 CDT
I cracked it - the site http://swissparam.ch/ generated a proper topology for me.
Subject: namd-l: topology for monophosphate
Date: Tue, 5 Apr 2011 10:25:52 -1000
I'm trying to define a phosphate residue for NAMD. I found this entry on a CHARMM forum from a few years ago:
RESI PHOS -2.00 ! Phosphate ion, dianionic; Gianluca Interlandi
GROUP ! H1
ATOM P1 P 1.040 ! |
ATOM O1 ON4 -0.680 ! O1
ATOM O2 ON3 -0.900 ! |
ATOM O3 ON3 -0.900 ! (-) O4==P1==O3 (-)
ATOM O4 ON3 -0.900 ! ||
ATOM H1 HN4 0.340 ! O2
BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 H1
IC O3 P1 O1 H1 0.0000 000.00 000.0 000.00 0.0000
IC O4 P1 O1 H1 0.0000 000.00 000.0 000.00 0.0000
IC O2 P1 O1 H1 0.0000 000.00 000.0 000.00 0.0000
! dummies to analyze cetain angles
IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0
When I try that, the Os form a tetrahedron, but the P is not in its center - it's off to one side. So I used the coordinates of phosphate from my starting pdb file, added an H in a builder, minimized it & filled in the bond, angle & dihedral values explicitly. I also tried giving no IC & using AUTO ANGLES DIHE instead. The P obstinately avoids being the central atom. I also tried making P atom 2 in the list, with O1 being the first. No change in behavior at all.
I also found a reference to a PNAS paper, where the citer suggested the topology ought to be in the supplemental materials. As far as I can tell, the SM consists of 3 figures only.
Could someone please help me debug this?
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:05 CST