[gmx-users] Error in pdb2gmx
Tsjerk Wassenaar
tsjerkw at gmail.com
Wed Aug 13 07:51:45 CEST 2008
Hi Vivek,
I downloaded 3bzu.pdb and ran the sorting on it as I described before
(sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
3bzu.pdb | sort | cut -b 2-), and it worked perfectly for me. I don't
see how you'd end up with some atoms inbetween other residues. It
seems as if the sorting counts space > number.
I do see another problem though, which is more fundamental to your
initial problem. The resason for not having consecutive chain
identifiers is that all hetatms are placed at the end of the atom
listing. If these hetatm residues are part of the same molecule, you'd
be on the right route (sorting and running pdb2gmx), but you'll have
to make sure you have building block descriptions. If these are not
part of the same molecule, you better remove them from the file before
running pdb2gmx, make topology include files for each separate
molecule and combine these later on. If you don't understand what I'm
talking about, don't do it; pick another protein.
Cheers,
Tsjerk
On Wed, Aug 13, 2008 at 7:37 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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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>>> >
>>> > --
>>> > ========================================
>>> >
>>> > 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
>
--
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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