Yi Gao wrote:
Hi, I used x2top to generate spc216.top. The spc216.gro file comes from
Gromacs tutor directory. I use Gromacs 4.0.5 version. The command line
is x2top -f scp216.gro -o scp216.top. The error message is
Can not find forcefield for atom OW-1 with 2 bonds
Can not find forcefield for atom OW-4 with 2 bonds
Can not find forcefield for atom OW-7 with 2 bonds
Can not find forcefield for atom OW-10 with 2 bonds
Can not find forcefield for atom OW-13 with 2 bonds
Can not find forcefield for atom OW-16 with 2 bonds
Can not find forcefield for atom OW-19 with 2 bonds
Can not find forcefield for atom OW-22 with 2 bonds
Can not find forcefield for atom OW-25 with 2 bonds
Can not find forcefield for atom OW-28 with 2 bonds
Can not find forcefield for atom OW-31 with 2 bonds
Can not find forcefield for atom OW-34 with 2 bonds
Can not find forcefield for atom OW-37 with 2 bonds
...
-------------------------------------------------------
Program x2top, VERSION 4.0.5
Source code file: x2top.c, line: 207
Fatal error:
Could only find a forcefield type for 432 out of 648 atoms
-------------------------------------------------------
I don't want to use pdb2gmx to generate *.top file, because spc216 water
is just a part of my system. Could anyone help me to resolve this
problem? Thanks a lot!
There is no need to do any of this. Just #include "spc.itp" in your topology.
See the manual for details, as well as:
http://www.gromacs.org/Documentation/Include_File_Mechanism
-Justin
Best,
Yi
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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