[gmx-users] grompp problem !

liu xin zgxjlx at gmail.com
Wed Dec 7 12:03:21 CET 2005

Dear gmx-users,

I'm trying to do a minimization of a protein/lipid system, but I get the
following eroor message when I do grompp:

merge.top:27:13: warning: no newline at end of file
Fatal error: number of coordinates in coordinate file (merge.gro, 22404)
does not match topology (merge.top, 20495).

My protein contain 5039 atoms, but in the protein.itp there's just 3130
atoms, I notice that 22404 - 20495 = 5039 - 3130, it seems that the
protein.itp misses some atoms. I generate the protein.itp by the following
steps: pdb2gmx -f -ignh -ter protein.pdb -o protein.gro -p protein.top,
then choose the "0: Gromacs Forcefield (see manual)", and select "none" when
asked to "Select C/N-terminus type", finally I rename the protein.top to
protein.itp and include it into the topology file.

I serched the mailing list, some one said it probably had something to do
with the cpp, but I don't know how to adjust it, could anybody so kind tell
me how to solve this problem? I use SUSE 9.2 and gromacs version 3.1.4.

Xin Liu
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