[gmx-users] NME, ACE

[Nagy, Peter I.]

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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