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Parameter Set Discussion Jump to new posts
Re: question generating forcefield parameters lennart 03/18/23 05:11 PM
What is the difference between a RESI and a PRES? And how is this related to READ SEQUENCE? The PATCh command is also relevant in this context.
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Installation and Testing Jump to new posts
Re: Installation of c48 on ubuntu 22.04 rmv 03/15/23 12:36 AM
The default gcc on Ubuntu 22 is version 11, so another possibility is the environment was not set up correctly, either for the 9.5 compiler, or for CUDA.

After the compiler environment is set up, what is the result of the command 'gcc --version' ?
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Parameter Set Discussion Jump to new posts
Parameters for non-carbonyl double bond in 4-membered ring clarexiong 02/23/23 03:55 PM

I am trying to generate the parameters for the ligand in cgenff website. The ligand contains a 4-mem ring with non-carbonyl double bond, but the non-carbonyl double bond in 4-membered ring is not supported in cgenff. So, I try to upload a similar ligand to generate the parameters and change the atom type to the original ligand. Then I use the CHARMM-GUI to get the input file for gromacs, it dosen't work out, it says there are parameters missed. I am wondering what else I should do to solve the issue. Thanks a lot.
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Installation and Testing Jump to new posts
Re: building in docker container bucknerj 02/22/23 07:24 PM
Is it possible for you to post steps to do this from scratch? I would be interested in making charmm compatible with musl and Alpine linux.

The backtrace stuff isn't particularly important. You could pop open source/machdep/cstuff.c and comment out the #include and the contents of the stacktrace function without harming the simulation stuff.

On certain platforms, in certain error/fail situations, stacktrace is supposed to provide something that looks like a backtrace. Sort of like when you compile with '-g' and have a segfault.
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CHARMM-GUI Jump to new posts
Re: Error when rerunning charmm-gui generated input rmv 02/21/23 05:33 PM
The charmm-gui output indicates the use of c47a2, which has newer code for AUTOGEN that older versions do not.

You probably cannot repeat that run w/o a charmm upgrade to a c47b release.
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