RE: topology for monophosphate

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.
 
Irene
 

From: einew_at_hotmail.com
To: namd-l_at_ks.uiuc.edu
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
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?

Thanks!
Irene Newhouse
                                               

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