Re: Using preprotonated structure with NAMD

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Tue Jul 28 2009 - 11:03:23 CDT

Most likely, there are mismatches in the atom naming scheme in your
original PDB file and the CHARMM residue topology files. For example,
the backbone hydrogen is called "HN" and not "H".

Giacomo

---- ----
 Giacomo Fiorin
   Center for Molecular Modeling at
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On Tue, Jul 28, 2009 at 10:48 AM, DimitryASuplatov<genesup_at_gmail.com> wrote:
> 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
>
>

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