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D-peptides in GROMACS
#37774 12/08/19 08:25 AM
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Mohsen Offline OP
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Hello
I want to simulate interaction of D-peptides with some proteins using MD and CHARMM force field.
As you know, the CHARMM force field for GROMACS is provided by MacKerell lab:
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

Does the parameters of D-peptides are provided in CHARMM? and Does these parameters exist in the files of MacKerell lab?

Re: D-peptides in GROMACS
Mohsen #37776 12/08/19 04:08 PM
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The files distributed in the toppar directory in the original format do contain D amino acids--

Code:
% ls stream/prot
toppar_all36_prot_aldehydes.str          
toppar_all36_prot_arg0.str
toppar_all36_prot_c36_d_aminoacids.str   
toppar_all36_prot_c36m_d_aminoacids.str
toppar_all36_prot_fluoro_alkanes.str     
toppar_all36_prot_heme.str
toppar_all36_prot_model.str              
toppar_all36_prot_modify_res.str
toppar_all36_prot_na_combined.str        
toppar_all36_prot_pyridines.str
toppar_all36_prot_retinol.str


A stream file for the recent c36m protein FF is available, as well as one for the older c36 FF. The residue names all have the letter D added, the chiral Calpha configuration is inverted, and the CMAP correction is modified accordingly.

I do not know if they are included in the GROMACS conversion, however.


Rick Venable
computational chemist

Re: D-peptides in GROMACS
Mohsen #37777 12/08/19 10:34 PM
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It is of course always possible to use CHARMM for the simulations...


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

Moderated by  alex, chmgr, John Legato 

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