Hello,
I am new to gromacs. I am applying the pdb2gmx tool to a peptide that
has an N-term pyroglutamate and a C-term amidation. The OPLS
forcefield has an entry for PGLU.
I used the -ter flag of pdb2gmx to define protonation states of the
termini. While this works fine for the C-term (choosing 3:None) I run
into trouble with the PGLU at the N-term.
In my input pdb the nitrogen of PGLU is attached to CA, CD and one
proton.
However when prompted 'Select start terminus type for PGLU-1' there is
no NH option. If I select 'None' I get "Fatal error: There is a
dangling bond at at least one of the terminal ends." If I chose NH2 I
end up with too many protons at my N-terminus.
If I leave out the -ter flag altogether I get problems with my C-
terminus: "Fatal error: atom C not found in building block 23NH2 while
combining tdb and rtp".
How would I solve this?
Regards,
Henry
--------------------------------------------------------
Henry Hocking, PhD
Utrecht University
Bijvoet Center for Biomolecular Research
Padualaan 8
3584 CH Utrecht, The Netherlands
Phone: +31-30-2532875
Fax: +31-30-253 7623
E-mail: h.g.hock...@uu.nl
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