RE: PSFGEN Warnings about H positions on standard amino acids

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Mon Feb 18 2008 - 18:17:48 CST

Bo,

   I get this type of error when a coordinate is not in the input
structure (which is usual for hydrogens in proteins), and when there are
no IC records in the topology file that unambiguously specify a three
dimensional position for the guessed atom, relative to the atoms with
definite coordinates (i.e., heavy atoms). The warnings for HN1/HN2 on
Pro1027 and HT1/HT2/HT3 on Ala2003 are expected if you're patching an
N-terminal residue.
 The LEU record in the topology file I use (also CHARMM27) has the
following IC records:

IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979
IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184
IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463
IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299
IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467
IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543
IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824
IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472
IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145
IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126
IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361
IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360
IC CD1 CD2 *CG HG 1.5361 110.2600 116.6300 108.0200 1.1168
IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111
IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112
IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108
IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116
IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086
IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115

For PRO,

IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624
IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399
IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569
IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316
IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517
IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399
IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837
IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322
IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317
IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131
IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088
IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077
IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143
IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137
IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144

If you're missing one or more of these lines, try pasting them into the
topology file (in mine, after the ACCEPTOR record) and repeating.
   My IC record for GLUP (Glu HE2 patch) is weird:

IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000

if yours is the same, you might try editing it to give more realistic
values prior to building the structure.

- Chris

Christopher H. Chang, Ph.D.
Scientist II
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007
 

> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu
> [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Bo Zhang
> Sent: Monday, February 18, 2008 6:08 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: PSFGEN Warnings about H positions on
> standard amino acids
>
> Hi,
>
> I am trying to generate PSF using auto psf generator in VMD. I get the
> following warnings about Hs added to standard amino acid residues. The
> topology file is Charmm27. The LEU and PRO residue sections seem
> fine. I tried using the topology file supplied with VMD and I get the
> same msgs. I am assuming that minimization in NAMD with sort out any
> poorly positioned hydrogens, but I just wondered what could be
> causing this?
>
> Thanks in advance
>
> Bo Zhang
>
>
> Info: guessing coordinates for 3612 atoms (0 non-hydrogen)
> Warning: poorly guessed coordinates for 49 atoms (0 non-hydrogen):
> Warning: poorly guessed coordinate for atom HN1 PRO:1027 P1
> Warning: poorly guessed coordinate for atom HN2 PRO:1027 P1
> Warning: poorly guessed coordinate for atom HG LEU:1037 P1
> Warning: poorly guessed coordinate for atom HG LEU:1058 P1
> Warning: poorly guessed coordinate for atom HG LEU:1059 P1
> Warning: poorly guessed coordinate for atom HG LEU:1067 P1
> Warning: poorly guessed coordinate for atom HG LEU:1079 P1
> Warning: poorly guessed coordinate for atom HG LEU:1098 P1
> Warning: poorly guessed coordinate for atom HG LEU:1100 P1
> Warning: poorly guessed coordinate for atom HG LEU:1121 P1
> Warning: poorly guessed coordinate for atom HG LEU:1131 P1
> Warning: poorly guessed coordinate for atom HG LEU:1138 P1
> Warning: poorly guessed coordinate for atom HG LEU:1139 P1
> Warning: poorly guessed coordinate for atom HG2 PRO:1147 P1
> Warning: poorly guessed coordinate for atom HG LEU:1151 P1
> Warning: poorly guessed coordinate for atom HG LEU:1154 P1
> Warning: poorly guessed coordinate for atom HG2 PRO:1166 P1
> Warning: poorly guessed coordinate for atom HG2 PRO:1173 P1
> Warning: poorly guessed coordinate for atom HG LEU:1188 P1
> Warning: poorly guessed coordinate for atom HG LEU:1214 P1
> Warning: poorly guessed coordinate for atom HG LEU:1215 P1
> Warning: poorly guessed coordinate for atom HG LEU:1227 P1
> Warning: poorly guessed coordinate for atom HG LEU:1241 P1
> Warning: poorly guessed coordinate for atom HG LEU:1249 P1
> Warning: poorly guessed coordinate for atom HG LEU:1281 P1
> Warning: poorly guessed coordinate for atom HG LEU:1283 P1
> Warning: poorly guessed coordinate for atom HG LEU:1284 P1
> Warning: poorly guessed coordinate for atom HG LEU:1295 P1
> Warning: poorly guessed coordinate for atom HG LEU:1311 P1
> Warning: poorly guessed coordinate for atom HG LEU:1316 P1
> Warning: poorly guessed coordinate for atom HG LEU:1333 P1
> Warning: poorly guessed coordinate for atom HE2 GLU:1338 P1
> Warning: poorly guessed coordinate for atom HG LEU:1343 P1
> Warning: poorly guessed coordinate for atom HG LEU:1354 P1
> Warning: poorly guessed coordinate for atom HG LEU:1360 P1
> Warning: poorly guessed coordinate for atom HT1 ALA:2003 P2
> Warning: poorly guessed coordinate for atom HT2 ALA:2003 P2
> Warning: poorly guessed coordinate for atom HT3 ALA:2003 P2
> Warning: poorly guessed coordinate for atom HG LEU:2008 P2
> Warning: poorly guessed coordinate for atom HG2 PRO:2020 P2
> Warning: poorly guessed coordinate for atom HG LEU:2035 P2
> Warning: poorly guessed coordinate for atom HG LEU:2043 P2
> Warning: poorly guessed coordinate for atom HG2 PRO:2047 P2
> Warning: poorly guessed coordinate for atom HG2 PRO:2048 P2
> Warning: poorly guessed coordinate for atom HG LEU:2052 P2
> Warning: poorly guessed coordinate for atom HG2 PRO:2064 P2
> Warning: poorly guessed coordinate for atom HG LEU:2071 P2
> Warning: poorly guessed coordinate for atom HG LEU:2095 P2
> Warning: poorly guessed coordinate for atom HG2 PRO:2096 P2
> Info: writing psf file mmroot_autopsf_tmpfile.psf
> total of 7364 atoms
> total of 7466 bonds
> total of 13480 angles
> total of 19839 dihedrals
> total of 1250 impropers
> total of 0 cross-terms
> Info: psf file complete.
> Info: writing pdb file mmroot_autopsf_tmpfile.pdb
> Info: Atoms with guessed coordinates will have occupancy of 0.0.
> Info: pdb file complete.
> Autopsf: Updating structures
> Autopsf: Updating structures
> Autopsf: Updating structures
> Loading the structure for rotation...
> Autopsf: Updating structures
>
>

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