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. -- * BISHWAJIT DAS*** KOLKATA
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