GROMACS version: 2018.04
GROMACS modification: Yes/No
Recently I performed tip4p/2005 bulk water simulation and in doing that I got error in generating the topology file for which I created the file called bulkwat_oplsaa.ff in the same directory where I was working. Here I am providing the command that I used to generate the topology for my work.
And I believe the problem is with the n2t file.
gmx x2top -f tip4p.gro -o topol.top -ff select -name tip4p -noparam
and the error that I got
Select the Force Field:
From current directory:
2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
Opening force field file ./bulkwat_oplsaa.ff/atomnames2types.n2t
There are 6 name to type translations in file ./bulkwat_oplsaa.ff
Generating bonds from distances…
Can not find forcefield for atom OW-1 with 0 bonds
Can not find forcefield for atom HW1-2 with 0 bonds
Program: gmx x2top, version 2018.3
Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 205)
Could only find a forcefield type for 0 out of 864 atoms
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
I know this is an old and reported problem, but I need to know what to do and where I was wrong. Along with that I used the other way and it worked that has been given in one of gromacs tip4p/ew simulation on the website.
It would be of great help for me if anybody can let me understand the problem associated with it.
Thanks and Regards,