search

Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
Other
261 stars 59 forks source link

Ligand parameters with CHARMM #975

Closed smar966 closed 4 years ago

smar966 commented 4 years ago

Hello! I'm having problems setting up the ligand parameters with a charmm force field. I normally use AMBER and add the ligand by defining the MOL2, PREPI and frcmod_lig for the ligand, and everything was working well with amber.build. Is there an easy way to convert these files into charmm compatible parameter files? On top of this, I am using the modified charmm36m, for which I have parameters that are working for the protein alone. Just to show you, I tried to build my topology as:

topos = ['top/top_all36_prot.rtf', 'top/top_water_ions.rtf', 'ff_parameters/tmp.prepi'] params = ['ff_parameters/par_all36m_prot.prm', 'par/par_water_ions.prm', 'ff_parameters/frcmod_lig']

molbuilt = charmm.build(smol, outdir='./build1/', saltconc=0.1, param=params_charmm, topo=topos_charmm) molbuilt.view()

Thank you in advance!

stefdoerr commented 4 years ago

Yes you will have to do the conversion from ligand AMBER parameters yourself. Proteins are ok. Some tools that do conversions are parmed and acpype. Possibly there are more which I don't know of.

smar966 commented 4 years ago

OK. I was hoping that there would be come conversion tool in HTMD, but it's alright. Thanks anyway! ;)