[gmx-users] Error in pdb2gmx
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Aug 13 07:37:53 CEST 2008
Hi Vivek,
Sorry, I should've been more careful. Sorting will obviously take the
rest of the line in account. I'll send a proper solution in a few
moments...
Cheers,
Tsjerk
On Wed, Aug 13, 2008 at 7:33 AM, vivek sharma
<viveksharma.iitb at gmail.com> wrote:
> Thanx David and Tsjerk,
> I tried the option given by Tsjerk on pdb file, then pdb2gmx command on
> sorted pdb file was giving the following error.
> Sorting it all out...
> Opening library file /usr/share/gromacs/top/
> ffG43a1.hdb
> Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb
> Opening library file /usr/share/gromacs/top/ffG43a1-c.tdb
> Processing chain 1 'A' (2108 atoms, 601 residues)
> There are 393 donors and 383 acceptors
> There are 533 hydrogen bonds
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: hizzie.c, line: 267
>
> Fatal error:
> Incomplete ring in HIS194
> -------------------------------------------------------
>
> Here I am attaching the sorted.pdb file, it is having some amino acids
> inserted between some other amino acid as below
> text from sorted pdb shows GLN and GLU are inserted in HIS
>
> ATOM 793 CD2 PHE A 129 -1.911 -9.897 3.599 1.00 43.21
> C
> ATOM 794 CE1 PHE A 129 -1.839 -11.242 5.997 1.00 41.19
> C
> ATOM 795 CE2 PHE A 129 -2.911 -10.794 3.911 1.00 41.19
> C
> ATOM 796 CZ PHE A 129 -2.874 -11.465 5.104 1.00 42.09
> C
> ATOM 797 N HIS A 130 1.739 -11.572 3.175 1.00 54.14
> N
> ATOM 798 CA HIS A 130 1.520 -12.688 2.246 1.00 55.63
> C
> ATOM 799 C HIS A 130 0.177 -13.421 2.474 1.00 55.34
> C
> ATOM 79 CD GLN A 33 8.099 10.312 47.238 1.00 69.55
> C
> ATOM 7 CD GLU A 25 -0.646 19.004 39.566 1.00 87.49
> C
> ATOM 800 O HIS A 130 -0.859 -13.049 1.913 1.00 56.40
> O
> ATOM 801 CB HIS A 130 2.726 -13.659 2.201 1.00 56.33
> C
> ATOM 802 CG HIS A 130 3.542 -13.730 3.467 1.00 58.59
> C
> ATOM 803 ND1 HIS A 130 4.249 -12.655 3.970 1.00 60.95
> N
> ATOM 804 CD2 HIS A 130 3.828 -14.777 4.284 1.00 59.58
> C
> ATOM 805 CE1 HIS A 130 4.895 -13.022 5.066 1.00 60.24
> C
> ATOM 806 NE2 HIS A 130 4.657 -14.305 5.279 1.00 60.16
> N
> ATOM 807 N ASP A 131 0.207 -14.462 3.285 1.00 54.76
> N
> ATOM 808 CA ASP A 131 -0.954 -15.320 3.512 1.00 54.01
> C
> ATOM 809 C ASP A 131 -1.040 -15.548 4.997 1.00 51.90
> C
> ATOM 80 OE1 GLN A 33 7.692 11.421 46.868 1.00 70.33
> O
>
> Kindly suggest any way to correct the .pdb file so that it can be converted
> to .gro file
>
> With Thanx,
> Vivek
>
> 2008/8/12 Tsjerk Wassenaar <tsjerkw at gmail.com>
>>
>> Well,
>>
>> sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
>> file.pdb | sort | cut -b 2- > sorted.pdb
>>
>> sort of seems to do the trick. But it will place the chainless things
>> first.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> >
>> >
>> > vivek sharma wrote:
>> >>
>> >> Hi david,
>> >> Thanx again, but I want to ask what changes need to be done there in
>> >> such
>> >> cases.
>> >>
>> >
>> > The chain identifier needs to be continuous. That is, if you have atoms
>> > with chain identifiers like:
>> >
>> > A
>> > A
>> > B
>> > A
>> > C
>> > A
>> > A
>> >
>> > they should be re-written as:
>> >
>> > A
>> > A
>> > A
>> > A
>> > A
>> > B
>> > C
>> >
>> > This can be accomplished with some work in a simple text editor.
>> >
>> > -Justin
>> >
>> >> With Thanx,
>> >> Vivek
>> >>
>> >> 2008/8/12 David van der Spoel <spoel at xray.bmc.uu.se
>> >> <mailto:spoel at xray.bmc.uu.se>>
>> >>
>> >> vivek sharma wrote:
>> >>
>> >> Hi David,
>> >> Thanks for the quick reply. My apologies for asking you again a
>> >> silly doubt as, I am doing this all for the first time. It will
>> >> be of great help if you can tell me how to do such correction
>> >> manually.
>> >>
>> >>
>> >> with a text editor, like emacs, notepad or whatever.
>> >>
>> >>
>> >> With Thanx,
>> >> Vivek
>> >>
>> >> 2008/8/12 David van der Spoel <spoel at xray.bmc.uu.se
>> >> <mailto:spoel at xray.bmc.uu.se> <mailto:spoel at xray.bmc.uu.se
>> >> <mailto:spoel at xray.bmc.uu.se>>>
>> >>
>> >>
>> >> vivek sharma wrote:
>> >>
>> >> Hello there,
>> >> I am trying to run pdb2gmx on 3bzu.pdb file and got the
>> >> following error
>> >>
>> >> Opening library file /usr/share/gromacs/top/
>> >> ffG43b1.rtp
>> >> Opening library file
>> >> /usr/share/gromacs/top/aminoacids.dat
>> >> Reading 3bzu.pdb...
>> >> WARNING: all CONECT records are ignored
>> >> Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6
>> >> BETA-HSD1', 8581 atoms
>> >> Opening library file /usr/share/gromacs/top/xlateat.dat
>> >> 26 out of 26 lines of xlateat.dat converted succesfully
>> >> Analyzing pdb file
>> >>
>> >> -------------------------------------------------------
>> >> Program pdb2gmx, VERSION 3.3.3
>> >> Source code file: pdb2gmx.c, line: 878
>> >>
>> >> Fatal error:
>> >> Chain identifier 'A' was used in two non-sequential
>> >> blocks
>> >> (residue 1034, atom 7961)
>> >> -------------------------------------------------------
>> >> as I am new to this field. I'm finding it very difficult
>> >> to
>> >> find the reason and rectify it.
>> >> Any suggestion would be of great help......
>> >>
>> >> This is a limitation in pdb2gmx. It expects the atoms in the
>> >> chain
>> >> A to be in sequence in the pdb file. You can manually sort
>> >> the pdb
>> >> file on the chain identifier.
>> >>
>> >>
>> >> With Thanx,
>> >> Vivek
>> >>
>> >>
>> >> ------------------------------------------------------------------------
>> >>
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>> >>
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>> >
>> > --
>> > ========================================
>> >
>> > Justin A. Lemkul
>> > Graduate Research Assistant
>> > 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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>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> Junior UD (post-doc)
>> Biomolecular NMR, Bijvoet Center
>> Utrecht University
>> Padualaan 8
>> 3584 CH Utrecht
>> The Netherlands
>> P: +31-30-2539931
>> F: +31-30-2537623
>> _______________________________________________
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>
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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