[email protected] wrote:
Hi,
I am trying to use the CHARMM27 force field to Gromacs to simulate two
proteins unite with command -merge, but the following error message is
coming:
"Opening library file
/storage2/rgr/software/gromacs/share/gromacs/top/aminoacids.dat
WARNING: atom C is missing in residue LYSH 16 in the pdb file
WARNING: atom C is missing in residue LYSH 32 in the pdb file
-------------------------------------------------------
Program pdb2gmx_d, VERSION 3.3.3
Source code file: pdb2top.c, line: 697
Fatal error:
There were 2 missing atoms in molecule Protein_A, if you want to use this
incomplete topology anyhow, use the option -missing
-------------------------------------------------------"
Can you help me? See you soon.
http://oldwiki.gromacs.org/index.php/Errors#Long_bonds_and.2For_missing_atoms
-Justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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