[gmx-users] problem with using pdb2gmx on a single amino acid

[Justin A. Lemkul]

Joe Joe wrote:
> I think there is a tdb problem when using pdb2gmx on a single amino 
> acid. The tdb databases replaces the CA with different charges depending 
> on whether its a c or n termini. When its a single amino acid you get 
> the c terminal charge and thus the overall charge is incorrect. Am I 
> missing something?

That will depend somewhat on which force field you're using.  A quick look at 
ffG53a6-n/c.tdb indicates there should be no conflict; CA is only replaced in 
the -n.tdb file, there is no competing CA replacement in -c.tdb.  In OPLS, you 
just have to be sure you're choosing the zwitterion form for each terminus 
(since you have a zwitterionic single amino acid), or else you will get conflict.

-Justin

> 
> Thanks,
> 
> Ilya
> 

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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