GROMACS version: 2018.04
GROMACS modification: Yes/No
hello,
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:
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…
…
1
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
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 ]
water
[ molecules ]
SOL X
where X is the number of water molecules you have in the system.
Hello,
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 topol.top -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
Marco
Yes, because its default settings apparently do not cover any of the required connectivity of your molecule(s).
Following this discussion, I have a question related to this topic I am using charmm36 that uses units of angstorm for bond lengths etc and in Gromacs the units are usually in nm. So whether the bond length in n2t file should be set in angstorm( according to the force field) or in nanometer as per gromacs units. I am unable to find detailed discussion on n2t file. If someone could guide about this it would be of great help.
Regards,
Aqsa
GROMACS uses SI units for everything; this convention has nothing to do with any individual force field.
The format of a line in an .n2t file is as follows:
- Element
- Atom type to be assigned
- Charge to be assigned
- Mass of the atom
- Number of bonded neighbors
- (and beyond) Pairs of elements and their associated distances from the atom being searched (number of pairs you find is specified in field 5)
gmx x2top will find the best match for a given atom based on what you specify as options, and assign those atom types and charges. It makes no attempt to “sanity check” any of those assignments. It assumes what you have provided it will work properly. It will bail out with an error if no match can be made. Remember that all GROMACS distance searches have a ±10% tolerance (relevant for the specification of bonded distances in fields 7 and onward).
Thank you for your reply sir. The problem I was facing is that I generated a .n2t file for boron nitride, generated it’s topology and even ran the Md simulation but when the results came back the sheet was crumbled. I searched a lot and found the bond length I defined in .n2t file were in nm, where as the force field itself utilizes lengths in angstorm, so I wanted to ask if the bond lengths that we define in the n2t file should be in angstorm(using charmm36 ) or it should be in nm as I have done earlier as per the standard units of GROMACS.And if this could be a possible reason for the collapse of nanosheet.
Thank you for your time.
If you used Å as the unit, you would get a nonsensical topology, if one can even be generated. If you used nm, that is correct and the failure is due to some other issue. If this sheet is “infinite,” make sure you are using coordinates that are correctly positioned in a suitably sized box for running x2top with periodicity enabled, and in the .mdp settings, define periodic_molecules = yes to get the correct bonded representation.
@jalemkul Thank you very much for the detailed reply sir.The problem was in non-bonded parameters that I had defined for boron nitride now the sheet is normal.I had another question related to the my system I am attaching a (poly-peptide with 8 monomer) to the nitrogen atom of nanosheet(covalent attachment) I obtained the parameter for polymer from cgenff then added the corresponding atom types and charges from the itp to my n2t file the monomer of the poly-peptide is histidine and it’s itp file has various hydrogen atom type along with carbon types with different charges I have added them all in the n2t file in the same sequence as in the itp since most these atom types are attached to carbon when topology is created using x2top wrong type of carbon and consequently wrong charge is assigned to the atom of my structure. I want you to note the hydrogen types as well as the nitrogen type NG2R51 in the topology file at line 134 it is supposed to be a NG2S1 nitrogen type with a -0.555 charge. There are many other atoms whose atom type was supposed to be different. How can I obtain correct topology.I am attaching the itp file(plh.itp) along with the ss of topology and n2t file.How can I make sure that correct atom types are assigned.
The screenshot of n2t file
The itp file from cgenff for 4 monomers
plh-1.log (30.5 KB)
(I have changed the extension as I was unable to upload the .itp file)
The topology file
Any pointer or guidance you could provide would be of great value. Any inconvenience is regretted.
