[AMBER] Patches for AmberTools18

From: viktor drobot <linux776.gmail.com>
Date: Wed, 10 Apr 2019 14:26:12 +0300

Hello, dear community! I've prepared two patches - for memembed Makefile
and for pdb4amber.py utility.

The first patch fixes problems with linking process of memembed
(actually adds -lpthread to LIBS).

The second patch fixes incorrect behavior of --nohyd option of pdb4amber
utility. Following /TRPCage tutorial/ we've found that PDB file with NMR
structure which is supplied in the /section 6/ (*nmr_struct_1.pdb*,
contains hydrogen atoms which names start with digits (perhaps VMD
yields incorrect PDB). Digging inside pdb4amber code has shown that mask
for hydrogen stripping is based on atom name rather than element type.
So I've suggested that using element type-based mask is better. I've
tested it on the PDB file mentioned above and things look great. Patch
is attached here.

Thank you all for your work!

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Received on Wed Apr 10 2019 - 04:30:02 PDT
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