[gmx-users] NME, ACE
David L. Bostick
dbostick at physics.unc.edu
Tue Jul 8 22:21:02 CEST 2003
Try changing NME to NAC. I believe gmx will recognize this. It's just the
naming... check the rtp file that you are using from the /top directory to
David Bostick Office: 262 Venable Hall
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On Tue, 8 Jul 2003, Nagy, Peter I. wrote:
> 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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