GROMACS modification: Yes/No
Here post your question
I was going prepare a simulation and modelling residues with virtual site interactions using the charmm36-jul2021.ff, but with pdb2gmx I have gotten the following error:
A dummy mass for type CT3 bonded to type C is required, but no virtual site
database (.vsd) files where found”
Indeed there is no *.vsd file present in the ff directory.
Furthermore, in the charmm36-feb2021.ff release the ffbonded.itp has a section [ constrainttypes ] under which constraints imposed for dummy atoms. This section is also missing from the jul2021 release.
I wonder, would it be safe to copy over the constrainttypes section for the feb2021 to jul2021 and also copy merged.vsd to jul2021.ff/aminoacid.vsd?
Virtual site information was omitted from the release you mentioned, but in principle you can copy it from the previous one. The same applies for the constraints. We plan to reintroduce these in an upcoming release of the force field.
The reason: virtual site data and the corresponding are not present in the upstream CHARMM force field distribution. @jalemkul, please correct me if I’m wrong.
Yeah, I have thought that I can copy over, the file and constraints, but I wanted to make sure if it would be correct and, sort of, draw attention to it.
thanks for the quick response
It should be safe to copy it but just be aware that this file is entirely a GROMACS construct and has nothing to do with the actual CHARMM force field, hence why it got left out of the new port, which was generated in a more automated fashion from the CHARMM force field files. We used to write one as a boilerplate entry from the charmm27.ff file, but we don’t test it in any way.
This a year later reply:
I followed Andras’s suggestions and have copied the merged.vsd file to the charmm36-jul2022 release, added the [ constrainttypes ] from the feb2021 rlease to the new ffbonded.itp.
Using gmx 2021.5, pdb2gmx and solvation went well but for the minimization for grompp I have gotten the following errors:
“virtual site MCH1 (Res ACE-23) has non-zero mass 7.5175 (state A) /
7.5175 (state B)
Check your topology.
virtual site MNZ1 (Res LYS-27) has non-zero mass 8.5155 (state A) /
8.5155 (state B)
Check your topology.”
Why dummy atoms MCH1, MNZ1,… got masses, while in the atomtypes.atp Vsite atoms have 0 mass definition?
Interestingly, when I use the feb2021 release of the charmm36m ff and the same version of gmx, the virtual site atoms still get the same high masses, but grompp and minimization and md go without errors.
I have checked back my older simulations using Vsites with CHARMM36 all-atom force field (November 2018) release and gmx 2016, obviously, had no errors either.