Re: [AMBER] Patches for AmberTools18

From: Hai Nguyen <>
Date: Wed, 10 Apr 2019 16:19:11 -0400

hi Viktor,

thank you for your patch for pdb4amber. I've made the change here:


On Wed, Apr 10, 2019 at 8:39 AM Stephan Schott <> wrote:

> Hi Viktor,
> Thanks for the effort. We are facing a new release of AmberTools in the
> next month or so. There are a lot of changes, and at least pthread for
> memembed is already in there ;D. For pdb4amber, I think you might be
> partially right. The issue is that in many pdbs, the element entry is not
> there, or is used for something else. Probably something like (@H= | @/H)
> would cover the whole spectrum. CC to Hai to see what he thinks.
> Cheers,
> El mié., 10 abr. 2019 a las 13:28, viktor drobot (<>)
> escribió:
>> Hello, dear community! I've prepared two patches - for memembed Makefile
>> and for 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!
> --
> Stephan Schott Verdugo
> Biochemist
> Heinrich-Heine-Universitaet Duesseldorf
> Institut fuer Pharm. und Med. Chemie
> Universitaetsstr. 1
> 40225 Duesseldorf
> Germany
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Received on Wed Apr 10 2019 - 13:30:02 PDT
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