VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Dec 21 2010 - 11:49:14 CST
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Hello:
With VMR 1.8.7 I am trying to generate psf for a protein ending with
amidated phenylalanine, using validated top_all27_prot_na.rtf. I tried
also 'source autopsf.tcl', using a recent script, before autopsf. It
always crashes with error: failed on end segment.
The pdf file ends with (here I tried separately chain D, renumbering
atoms) using the method for amber:
ATOM 80 HE2 PHE D 4 -31.197 22.536 3.559 1.00 0.00 4SG H
ATOM 81 HZ PHE D 4 -30.544 24.713 4.555 1.00 0.00 4SG H
ATOM 82 C CT2 D 5 -32.820 18.877 8.926 1.00 0.00 4SG C
ATOM 83 O CT2 D 5 -34.065 18.451 9.222 1.00 0.00 4SG O
ATOM 84 NT CT2 D 5 -31.788 18.180 9.397 1.00 0.00 4SG N
ATOM 85 HT2 CT2 D 5 -30.844 18.477 9.196 1.00 0.00 4SG H
ATOM 86 HT1 CT2 D 5 -31.949 17.354 9.956 1.00 0.00 4SG H
Is that correct?
Thanks for help
francesco pietra
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