[gmx-users] Fwd: pdb2gmx converting coordinates incorrectly.
William Welch
wwelch000 at gmail.com
Wed Sep 28 23:44:56 CEST 2011
---------- Forwarded message ----------
From: William Welch <wwelch000 at gmail.com>
Date: Wed, Sep 28, 2011 at 3:43 PM
Subject: pdb2gmx converting coordinates incorrectly.
To: gmxusers at gromacs.org
Friends,
I generated a pdb for a tyrosineamide molecule and made an entry for it in
ffcharmm27.rtp. Everything seems to be fucntional--I can make the .gro file
and the .top file using pdb2gmx and subsequent processes seem to execute
fine. The only problem is that when I look at the .gro file in VMD, I can
see that the atoms have been moved to entirely different coordinates with
respect to each other---I mean it's not even a real molecule, and certainly
not the one I'm starting with Looking at the text of the .gro file, I see
that the x cooridinate seems to have been converted correctly to nanometers,
but the y and z coordinates are clearly wrong. Here are copies of the
coordinates (the columns are aligned in the real files). This happens when
I use pdb2gmx Version 4.0.5
PDB
TITLE tyrosineamide2
REMARK 4
REMARK 4 COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996
REMARK 6 created by ArgusLab version 4.0.1
REMARK 6 http://www.arguslab.com
REMARK 6
ATOM 1 NH3 TYRA ? 1 -1.797 5.686
-1.030 N
ATOM 2 CA TYRA ? 1 -1.575 4.269
-0.716 C
ATOM 3 C TYRA ? 1 -0.273 3.854
-1.311 C
ATOM 4 O TYRA ? 1 0.570 3.201
-0.654 O
ATOM 5 CB TYRA ? 1 -2.734 3.441
-1.274 C
ATOM 6 CG TYRA ? 1 -3.924 3.374
-0.339 C
ATOM 7 CD1 TYRA ? 1 -3.942 2.496
0.665 C
ATOM 8 CD2 TYRA ? 1 -5.007 4.235
-0.538 C
ATOM 9 CE1 TYRA ? 1 -5.072 2.449
1.563 C
ATOM 10 CE2 TYRA ? 1 -6.152 4.156
0.320 C
ATOM 11 CZ TYRA ? 1 -6.140 3.253
1.299 C
ATOM 12 OH TYRA ? 1 -7.278 3.176
2.149 O
ATOM 13 NH2 TYRA ? 1 0.019 4.207
-2.655 N
ATOM 14 HA TYRA ? 1 -1.536 4.134
0.375 H
ATOM 15 HB1 TYRA ? 1 -3.064 3.890
-2.223 H
ATOM 16 HB2 TYRA ? 1 -2.380 2.416
-1.457 H
ATOM 17 HD1 TYRA ? 1 -3.096 1.808
0.810 H
ATOM 18 HD2 TYRA ? 1 -4.980 4.973
-1.354 H
ATOM 19 HE1 TYRA ? 1 -5.055 1.776
2.433 H
ATOM 20 HE2 TYRA ? 1 -7.007 4.829
0.160 H
ATOM 21 HH TYRA ? 1 -7.154 2.339
2.852 H
ATOM 22 HC1 TYRA ? 1 -0.899 6.265
-0.766 H
ATOM 23 HC2 TYRA ? 1 -2.656 6.059
-0.453 H
ATOM 24 HC3 TYRA ? 1 -2.000 5.796
-2.105 H
ATOM 25 HN1 TYRA ? 1 0.976 3.907
-3.107 H
ATOM 26 HN2 TYRA ? 1 -0.682 3.761
-3.376 H
.gro
tyrosineamide2
26
1TYRA NH3 1 -0.179 0.700 0.600
1TYRA HC1 2 -0.089 0.900 0.500
1TYRA HC2 3 -0.265 0.600 0.900
1TYRA HC3 4 -0.200 0.000 0.600
1TYRA CA 5 -0.157 0.500 0.900
1TYRA HA 6 -0.153 0.600 0.400
1TYRA CB 7 -0.273 0.400 0.100
1TYRA HB1 8 -0.306 0.400 0.000
1TYRA HB2 9 -0.238 0.000 0.600
1TYRA CG 10 -0.392 0.400 0.400
1TYRA CD1 11 -0.394 0.200 0.600
1TYRA HD1 12 -0.309 0.600 0.800
1TYRA CE1 13 -0.507 0.200 0.900
1TYRA HE1 14 -0.505 0.500 0.600
1TYRA CZ 15 -0.614 0.000 0.300
1TYRA OH 16 -0.727 0.800 0.600
1TYRA HH 17 -0.715 0.400 0.900
1TYRA CD2 18 -0.500 0.700 0.500
1TYRA HD2 19 -0.498 0.000 0.300
1TYRA CE2 20 -0.615 0.200 0.600
1TYRA HE2 21 -0.700 0.700 0.900
1TYRA C 22 -0.027 0.300 0.400
1TYRA O 23 0.057 0.000 0.100
1TYRA NH2 24 0.001 0.900 0.700
1TYRA HN1 25 0.097 0.600 0.700
1TYRA HN2 26 -0.068 0.200 0.100
0.82400 0.90000 0.90000
Will
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