[gmx-users] NME, ACE
Nagy, Peter I.
PNAGY at UTNet.UToledo.Edu
Tue Jul 8 22:16:02 CEST 2003
Dear Gromacs Users!
I am going to run a test job for two alpha helices, where each of them is
capped either with an N-CH3 or a CH3CO group. (Actually the two helices were obtained by cutting out a connecting loop). I gave the names NME and ACE for the end groups in the pdb file. The structure can be handled by the Sybyl software and appears correctly on the screen.
When I submitted this file to GROMACS as
pdb2gmx -f test.pdb
the system complained about the NME residue name (probably it would have
also complained for ACE, but NME appeared first and the job seemingly died
at that moment.)
I need to cap the ends of helices because I do not want them to be protonated at two N-termini and getting two carboxylates at the C-termini. What should I modify in the pdf file in order to make GROMACS handle the system properly?
Thanks, Peter Nagy
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