Dear Nan,
In your case - for pH conditions below the PKa value you indeed need
the carboxylic acid version of the C-terminal molecular fragment; and
as underlined by Dr Case the Amber force field (FF) topology database
does only contain the carboxylate fragment.
Generating the carboxylic acid version of the C-terminal molecular
fragment for the 20 amino-acids can represent a substantive work.
I would answer that your best bet is to start from a capped peptide:
CH3CO-NHCHRCOOH --> NHCHRCOOH
and generate the wanted NHCHRCOOH fragment by using a specific charge
constraint applied during the charge fitting step and by removing the
atoms involved in this constraint from the whole molecule.
Obviously other approaches are also possible...
You could use the R.E.D. tools and/or R.E.D. Server at
q4md-forcefieldtools.org to perform this task. you can find tutorials
there; see for instance:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#18
(pay attention the target is slightly different in this #18 tutorial part)
You can also find such a neutral terminal fragment in R.E.DD.B. as well
http://q4md-forcefieldtools.org/REDDB/
Just perform a search at:
http://q4md-forcefieldtools.org/REDDB/download.php
Result(s) for search by Molecule keyword HOOC-terminal fragment
regards, Francois
> I used xleap to add hydrogens to peptides (the peptide was loaded as
> pdb file without hydrogens) automatically. For the -COOH groups in the
> c-terminal, the Hydrogen is not added (the peptide ends with -COO). Is
> there any reason for xleap not to add hydrogen atom to -COO?
> Also, I checked the charge that is zero. Thanks a lot.
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Received on Wed Mar 06 2013 - 23:00:04 PST
