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<P><FONT SIZE=2>Dear Gromacs Users!<BR>
<BR>
I am going to run a test job for two alpha helices, where each of them is<BR>
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.<BR>
<BR>
When I submitted this file to GROMACS as<BR>
<BR>
pdb2gmx -f test.pdb<BR>
<BR>
the system complained about the NME residue name (probably it would have<BR>
also complained for ACE, but NME appeared first and the job seemingly died<BR>
at that moment.)<BR>
<BR>
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?<BR>
<BR>
Thanks, Peter Nagy</FONT>
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