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
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
