Hi Tom,
setting rtp and atp files is not sufficient in order to make a complete
topology in GMX. You have to added also some new bonds, angles,
dihidrals etc... in ff*bon.itp ff*nb.itp. Check all of this. Look at all
the files for one force field (ffG53a6.* in the top folder). They may
contain information that you have maybe missed.
But your problem may comes from elsewhere.....
Good luck
Hi all,
To work with PTR in gromacs I added the residue information in
ffG53a6.rtp, added the unknown atom names () to ffG53a6.atp and added
the residue name to aminoacids.dat.
this allowed me to make the topology file using pdb2gmx, create the
box and fill it with water. Now I want to perform the
energy minimisation by first doing grompp. Then
I get an error
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
Cleaning up temporary file grompp8BMpzT
-------------------------------------------------------
Program grompp, VERSION 3.3
Source code file: toputil.c, line: 61
Fatal error:
Atomtype 'CB' not found!
-------------------------------------------------------
Yet I added the atom CB to the ffG53a6.atp file ... so what can be the
problem here?
Tom
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