Hi everyone,
In the modeling protocol I am replicating, the authors do the following: "The TM is first parameterized with neutral termini using a cross-term energy correction map (CMAP) dihedral-corrected CHARMM27 forcefield (and 1 charge group per atom)".
To perform that, I am using GROMACS where I wrote the command:
gmx pdb2gmx -f odr10tms.pdb -o odr10tms_results.gro -water tips3p
Then chose the option 8 for "CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)".
But I'm not sure this is the correct form to procede, because 1. I am not parameterizing the "1 charge group per atom" part and 2. I read that GROMACS has an option for CHARMM27 that includes the CMAP correction for proteins.
Could you please tell me if I did it correctly? If not, what should I do?
I appreciate any advice and help with it.
Hello
there is a CHARMM27 force field, but not for proteins. C27 pertains to nucleic acids and lipids. The protein force field C22 was revised at the same time to include CMAP corrections and was bundled together with the C27 release (versioning based on the CHARMM program version with which the force field was released).So there is always some confusion.
This links can help you:
dx.doi.org/10.1021/jp101759q
dx.doi.org/10.1021/ct300400x
Jesus Durand Hi
You can use OPLS forcefield with TIP3 water model. OPLS forcefield parameterized all organic molecules.
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