Gmx x2top topology generation

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 -ff select -name tip4p -noparam

and the error that I got

Select the Force Field:
From current directory:

1: bulkwat_oplsaa

From ‘/usr/local/share/gromacs/top’:
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)
5: AMB…

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…
atom 864
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)

Fatal error:
Could only find a forcefield type for 0 out of 864 atoms

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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,

Anupama Sharma

The error means that the .n2t file does not specify bonded connectivity for water. Such files are not intended for building water topologies, which already exist in the force field subdirectory. A topology for pure water is trivial:

#include "oplsaa.ff/forcefield.itp"
#include "oplsaa.ff/tip4p.itp"
[ system ]
[ molecules ]
SOL    X

where X is the number of water molecules you have in the system.


I have got the same problem here. No water though.
I have a pdb and rtp files downloaded from the ATB server.

gmx x2top -f TFSI.pdb -o -r TFSI.rtp -ff oplsaa
Generating bonds from distances…
Can not find forcefield for atom F6-1 with 0 bonds

There are 23 name to type translations in file ./oplsaa.ff

Fatal error:
Could only find a forcefield type for 0 out of 15 atoms

Should I check the oplsaa.ff/atomname2type.n2t?
Thank you for your support


Yes, because its default settings apparently do not cover any of the required connectivity of your molecule(s).