<div dir="ltr">Thanx David and Tsjerk,<br> I tried the option given by Tsjerk on pdb file, then pdb2gmx command on sorted pdb file was giving the following error.<br>Sorting it all out...<br>Opening library file /usr/share/gromacs/top/<div dir="ltr">
ffG43a1.hdb<br>
Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb<br>Opening library file /usr/share/gromacs/top/ffG43a1-c.tdb<br>Processing chain 1 'A' (2108 atoms, 601 residues)<br>There are 393 donors and 383 acceptors<br>
There are 533 hydrogen bonds<div class="Ih2E3d"><br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 3.3.3<br></div>Source code file: hizzie.c, line: 267<br><br>Fatal error:<br>Incomplete ring in HIS194<br>
-------------------------------------------------------<br>
<br>Here I am attaching the sorted.pdb file, it is having some amino acids inserted between some other amino acid as below<br>text from sorted pdb shows GLN and GLU are inserted in HIS<br><br>ATOM 793 CD2 PHE A 129 -1.911 -9.897 3.599 1.00 43.21 C <br>
ATOM 794 CE1 PHE A 129 -1.839 -11.242 5.997 1.00 41.19 C <br>ATOM 795 CE2 PHE A 129 -2.911 -10.794 3.911 1.00 41.19 C <br>ATOM 796 CZ PHE A 129 -2.874 -11.465 5.104 1.00 42.09 C <br>
ATOM 797 N HIS A 130 1.739 -11.572 3.175 1.00 54.14 N <br>ATOM 798 CA HIS A 130 1.520 -12.688 2.246 1.00 55.63 C <br>ATOM 799 C HIS A 130 0.177 -13.421 2.474 1.00 55.34 C <br>
<span style="color: rgb(204, 0, 0);">ATOM 79 CD GLN A 33 8.099 10.312 47.238 1.00 69.55 C </span><br style="color: rgb(204, 0, 0);"><span style="color: rgb(204, 0, 0);">ATOM 7 CD GLU A 25 -0.646 19.004 39.566 1.00 87.49 C </span><br>
ATOM 800 O HIS A 130 -0.859 -13.049 1.913 1.00 56.40 O <br>ATOM 801 CB HIS A 130 2.726 -13.659 2.201 1.00 56.33 C <br>ATOM 802 CG HIS A 130 3.542 -13.730 3.467 1.00 58.59 C <br>
ATOM 803 ND1 HIS A 130 4.249 -12.655 3.970 1.00 60.95 N <br>ATOM 804 CD2 HIS A 130 3.828 -14.777 4.284 1.00 59.58 C <br>ATOM 805 CE1 HIS A 130 4.895 -13.022 5.066 1.00 60.24 C <br>
ATOM 806 NE2 HIS A 130 4.657 -14.305 5.279 1.00 60.16 N <br>ATOM 807 N ASP A 131 0.207 -14.462 3.285 1.00 54.76 N <br>ATOM 808 CA ASP A 131 -0.954 -15.320 3.512 1.00 54.01 C <br>
ATOM 809 C ASP A 131 -1.040 -15.548 4.997 1.00 51.90 C <br>ATOM 80 OE1 GLN A 33 7.692 11.421 46.868 1.00 70.33 O <br><br>Kindly suggest any way to correct the .pdb file so that it can be converted to .gro file<br>
<br>With Thanx,<br>Vivek</div><br><br><div class="gmail_quote">2008/8/12 Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Well,<br>
<br>
sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'<br>
file.pdb | sort | cut -b 2- > sorted.pdb<br>
<br>
sort of seems to do the trick. But it will place the chainless things first.<br>
<br>
Hope it helps,<br>
<br>
Tsjerk<br>
<div><div></div><div class="Wj3C7c"><br>
On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
><br>
><br>
> vivek sharma wrote:<br>
>><br>
>> Hi david,<br>
>> Thanx again, but I want to ask what changes need to be done there in such<br>
>> cases.<br>
>><br>
><br>
> The chain identifier needs to be continuous. That is, if you have atoms<br>
> with chain identifiers like:<br>
><br>
> A<br>
> A<br>
> B<br>
> A<br>
> C<br>
> A<br>
> A<br>
><br>
> they should be re-written as:<br>
><br>
> A<br>
> A<br>
> A<br>
> A<br>
> A<br>
> B<br>
> C<br>
><br>
> This can be accomplished with some work in a simple text editor.<br>
><br>
> -Justin<br>
><br>
>> With Thanx,<br>
>> Vivek<br>
>><br>
>> 2008/8/12 David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>
>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>><br>
>><br>
>> vivek sharma wrote:<br>
>><br>
>> Hi David,<br>
>> Thanks for the quick reply. My apologies for asking you again a<br>
>> silly doubt as, I am doing this all for the first time. It will<br>
>> be of great help if you can tell me how to do such correction<br>
>> manually.<br>
>><br>
>><br>
>> with a text editor, like emacs, notepad or whatever.<br>
>><br>
>><br>
>> With Thanx,<br>
>> Vivek<br>
>><br>
>> 2008/8/12 David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>
>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>
>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>>><br>
>><br>
>><br>
>> vivek sharma wrote:<br>
>><br>
>> Hello there,<br>
>> I am trying to run pdb2gmx on 3bzu.pdb file and got the<br>
>> following error<br>
>><br>
>> Opening library file /usr/share/gromacs/top/<br>
>> ffG43b1.rtp<br>
>> Opening library file /usr/share/gromacs/top/aminoacids.dat<br>
>> Reading 3bzu.pdb...<br>
>> WARNING: all CONECT records are ignored<br>
>> Read 'CORTICOSTEROID 11-BETA-DEHYDROGENASE ISOZYME 1; 6<br>
>> BETA-HSD1', 8581 atoms<br>
>> Opening library file /usr/share/gromacs/top/xlateat.dat<br>
>> 26 out of 26 lines of xlateat.dat converted succesfully<br>
>> Analyzing pdb file<br>
>><br>
>> -------------------------------------------------------<br>
>> Program pdb2gmx, VERSION 3.3.3<br>
>> Source code file: pdb2gmx.c, line: 878<br>
>><br>
>> Fatal error:<br>
>> Chain identifier 'A' was used in two non-sequential blocks<br>
>> (residue 1034, atom 7961)<br>
>> -------------------------------------------------------<br>
>> as I am new to this field. I'm finding it very difficult to<br>
>> find the reason and rectify it.<br>
>> Any suggestion would be of great help......<br>
>><br>
>> This is a limitation in pdb2gmx. It expects the atoms in the<br>
>> chain<br>
>> A to be in sequence in the pdb file. You can manually sort<br>
>> the pdb<br>
>> file on the chain identifier.<br>
>><br>
>><br>
>> With Thanx,<br>
>> Vivek<br>
>><br>
>> ------------------------------------------------------------------------<br>
>><br>
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> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Graduate Research Assistant<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
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<br>
<br>
<br>
</div></div>--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
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</div></div></blockquote></div><br></div>