[gmx-users] NME, ACE

[David L. Bostick]

HI,

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
see.

David

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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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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
>