Using preprotonated structure with NAMD

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Tue Jul 28 2009 - 09:48:18 CDT

Hello,

I have a structure with all hydrogens already added according to some
pH. So I do not want to use namd/vmd protonation utility to prepare my
structure. I comment out "guesscoord" command in the vmd script but when
I launch it for my structure I get this

Warning: failed to set coordinate for atom H1 LYS:1 1
Warning: failed to set coordinate for atom H2 LYS:1 1
Warning: failed to set coordinate for atom H PHE:2 1
Warning: failed to set coordinate for atom H ASP:3 1
Warning: failed to set coordinate for atom H THR:4 1
Warning: failed to set coordinate for atom H SER:5 1
Warning: failed to set coordinate for atom H ALA:6 1
Warning: failed to set coordinate for atom H LEU:7 1
Warning: failed to set coordinate for atom H GLU:8 1
Warning: failed to set coordinate for atom H ALA:9 1
Warning: failed to set coordinate for atom H PHE:10 1
Warning: failed to set coordinate for atom H VAL:11 1
Warning: failed to set coordinate for atom H ARG:12 1
Warning: failed to set coordinate for atom H HIS:13 1
Warning: failed to set coordinate for atom H ILE:14 1
Warning: failed to set coordinate for atom H GLN:16 1
Warning: failed to set coordinate for atom H ASN:17 1
Warning: failed to set coordinate for atom H TYR:18 1
Warning: failed to set coordinate for atom H LYS:19 1
Warning: failed to set coordinate for atom H GLY:20 1
Warning: failed to set coordinate for atom H GLY:22 1
Warning: failed to set coordinate for atom H GLY:23 1
Warning: failed to set coordinate for atom H VAL:24 1
Warning: failed to set coordinate for atom H VAL:25 1
Warning: failed to set coordinate for atom H ALA:26 1
Warning: failed to set coordinate for atom H VAL:27 1
Warning: failed to set coordinate for atom H VAL:28 1
Warning: failed to set coordinate for atom H LYS:29 1
Warning: failed to set coordinate for atom H ASP:30 1
Warning: failed to set coordinate for atom H GLY:31 1
Warning: failed to set coordinate for atom H GLU:32 1
Warning: failed to set coordinate for atom H VAL:33 1
Warning: failed to set coordinate for atom H VAL:34 1
Warning: failed to set coordinate for atom H LEU:35 1
Warning: failed to set coordinate for atom H GLN:36 1
Warning: failed to set coordinate for atom H HIS:37 1
Warning: failed to set coordinate for atom H ALA:38 1
Warning: failed to set coordinate for atom H TRP:39 1
Warning: failed to set coordinate for atom H GLY:40 1
Warning: failed to set coordinate for atom H PHE:41 1
Warning: failed to set coordinate for atom H ALA:42 1
Warning: failed to set coordinate for atom H ASP:43 1
Warning: failed to set coordinate for atom H LEU:44 1
Warning: failed to set coordinate for atom H ARG:45 1
Warning: failed to set coordinate for atom H THR:46 1
Warning: failed to set coordinate for atom H ARG:47 1
Warning: failed to set coordinate for atom H THR:48 1
Warning: failed to set coordinate for atom H MET:50 1
Warning: failed to set coordinate for atom H THR:51 1
Warning: failed to set coordinate for atom H LEU:52 1
Warning: failed to set coordinate for atom H ASP:53 1
Warning: failed to set coordinate for atom H THR:54 1
Warning: failed to set coordinate for atom H ARG:55 1
Warning: failed to set coordinate for atom H MET:56 1
Warning: failed to set coordinate for atom H ILE:58 1
Warning: failed to set coordinate for atom H CYS:59 1
Warning: failed to set coordinate for atom HG CYS:59 1
Warning: failed to set coordinate for atom O CYS:59 1

In particular this results in N-term-Lys backbone N not being protonated
at all! while other hydrogens are in the right place.

This is how Lys1 looked initially

ATOM 1 N LYS A 1 39.490 -13.940 -21.780 1.00 0.00
ATOM 2 H1 LYS A 1 38.610 -14.410 -21.880 1.00 0.00
ATOM 3 H2 LYS A 1 39.960 -14.270 -20.960 1.00 0.00
ATOM 4 CA LYS A 1 39.260 -12.460 -21.660 1.00 0.00
ATOM 5 HA LYS A 1 40.100 -12.010 -21.370 1.00 0.00
ATOM 6 CB LYS A 1 38.890 -11.840 -23.000 1.00 0.00
ATOM 7 HB1 LYS A 1 39.600 -12.100 -23.660 1.00 0.00
ATOM 8 HB2 LYS A 1 38.020 -12.240 -23.280 1.00 0.00
ATOM 9 CG LYS A 1 38.750 -10.330 -23.070 1.00 0.00
ATOM 10 HG1 LYS A 1 37.920 -10.060 -22.580 1.00 0.00
ATOM 11 HG2 LYS A 1 38.670 -10.050 -24.030 1.00 0.00
ATOM 12 CD LYS A 1 39.940 -9.610 -22.450 1.00 0.00
ATOM 13 HD1 LYS A 1 40.690 -10.260 -22.370 1.00 0.00
ATOM 14 HD2 LYS A 1 39.680 -9.300 -21.530 1.00 0.00
ATOM 15 CE LYS A 1 40.400 -8.420 -23.250 1.00 0.00
ATOM 16 HE1 LYS A 1 40.530 -8.710 -24.200 1.00 0.00
ATOM 17 HE2 LYS A 1 41.280 -8.120 -22.880 1.00 0.00
ATOM 18 NZ LYS A 1 39.480 -7.260 -23.230 1.00 0.00
ATOM 19 HZ1 LYS A 1 39.990 -6.420 -23.030 1.00 0.00
ATOM 20 HZ2 LYS A 1 38.780 -7.390 -22.530 1.00 0.00
ATOM 21 HZ3 LYS A 1 39.050 -7.180 -24.130 1.00 0.00
ATOM 22 C LYS A 1 38.170 -12.250 -20.620 1.00 0.00
ATOM 23 O LYS A 1 37.060 -12.760 -20.800 1.00 0.00

1/ What could be the problem?
2/ How can I use my protonated structure with namd?

Thank you for your time.
SDA

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:22:15 CST