[gmx-users] Fwd: pdb2gmx converting coordinates incorrectly.
Justin A. Lemkul
jalemkul at vt.edu
Thu Sep 29 00:16:34 CEST 2011
William Welch wrote:
>
>
> ---------- Forwarded message ----------
> From: *William Welch* <wwelch000 at gmail.com <mailto:wwelch000 at gmail.com>>
> Date: Wed, Sep 28, 2011 at 3:43 PM
> Subject: pdb2gmx converting coordinates incorrectly.
> To: gmxusers at gromacs.org <mailto: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
>
Your alignment is the problem. Compare the first line (from your file) with a
standard PDB file:
ATOM 1 NH3 TYRA ? 1 -1.797 5.686 -1.030 N
ATOM 1 N LYS 1 35.360 22.340 -11.980 1.00 0.00
You can easily see that the coordinates are going to be junk. The PDB format
requires fixed spacing. If this is not the case, you get unpredictable output.
-Justin
>
> 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
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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