Hi Fred, Since you're using CHARMM forcefield, another option is to use swissparam.ch . I don't know which system you're working on but I've recently used swissparam for multiple protein-ligand simulations.
Best, Tushar. On Sat, 22 May 2021, 21:13 Murpholino Peligro, <murpholi...@gmail.com> wrote: > Hi Fred.. > As an alternative, not mentioned yet, you can use NAMD ( > https://www.ks.uiuc.edu/Research/namd/). If I remember correctly it > accepts the charmm force fields. > I think the documentation is way better... > they also have a mailing list ... > As a plus... you can download a 'full' version without problems. > > El vie, 21 de may. de 2021 a la(s) 06:50, Fred Vellieux ( > frederic.velli...@lf1.cuni.cz) escribió: > >> Hi folks, >> >> Sorry about the non-ccp4 question. I don't know where to ask. >> >> I have to perform MD simulations but I am totally on my own here. The >> one program that appears to be free (in terms of license) seems to be >> CHARMM. GROMACS (testing with the examples found in the internet) did >> not work in my hands so I forget about that. >> >> Charmm somehow looks similar to a program I used to work with, X-PLOR. >> However I haven't found a manual similar to the old XPLOR manual nor a >> web site that can generate the input files as was the case for X-PLOR. >> Neither did I find anywhere a flow chart allowing me to know which steps >> to be performed and in what order. >> >> Hence: does anyone know of an X-PLOR to CHARMM dictionary ? Or a CHARMM >> bulletin board similar to CCP4BB ? >> >> Just to give an example using the CHARMM setup.inp file for a protein >> that has an "ACE" cap at the N-terminus: fails. It complains about the >> ACE cap. Removing the cap solves that problem but then CHARMM fails >> because of "HIS". If CHARMM fails because it doesn't like any >> amino-acids then I don't know how I can use the program. But still I'd >> like to use it because I have to. >> >> Thanks, >> >> Fred. >> >> -- >> MedChem, 1st F. Medicine, Charles University >> BIOCEV, Vestec, Czech Republic >> >> ######################################################################## >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
