[gmx-users] pdb2gmx error

Bishwajit Das das.bishwajit at gmail.com
Mon Apr 9 22:00:28 CEST 2012

when i try to  pdb2gmx -f *.pdb -o *_processed.gro -water spce command in
my pdb file then i select  AMBER99SB-ILDN force field (Lindorff-Larsen et
al., Proteins 78, 1950-58, 2010) this force field but a error massage came.
the massage is following:

There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue GLU6 as a starting terminus.
Identified residue GLU6 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Start terminus GLU-6: NH3+
End terminus GLU-6: COO-
Checking for duplicate atoms....

Program pdb2gmx, VERSION 4.5.4
Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pgutil.c, line: 88

Fatal error:
Atom CG not found in residue seq.nr. 1 while adding atom

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
 then i repair my protein with what if server as instruction given in
gromacs documentation...then i again run the above process but still
showing me a error massage.The massage was His 450 chain is not
complete.How i overcome this problem..please give me a suggestion.

Thanking You.

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