vivek sharma wrote:
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.
Sounds like the crystal structure has missing atoms. You'll need to reconstruct
the missing portions with a modeling program like DeepView or Modeller.
-Justin
With thanx,
Vivek
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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