Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command....
pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error..... ...... ...... ...... ....... N-terminus: NH3+ C-terminus: COO- WARNING: atom CE2 not found in residue 270 while adding atom ------------------------------------------------------- Program pdb2gmx, VERSION 3.3.3 Source code file: genhydro.c, line: 304 Fatal error: Atom CE2 not found in residue PHE270 while adding hydrogens ------------------------------------------------------- I tried the same with different force field and water models, but getting the same error again and again. any suggestion will be highly appreciated. With thanx, Vivek
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