Re: [AMBER] Signal: Segmentation fault (11)

From: David A Case <david.case.rutgers.edu>
Date: Sun, 25 Sep 2016 16:38:58 -0400

On Sun, Sep 25, 2016, shahab shariati wrote:
>
> The input file (lig.pdb) and the output files (lig.mol2, lig.lib and
> lig.frcmod) are as follows:
>
> https://cp.sync.com/dl/1fbba13a0#dq79chn2-7y5wnc8m-cpvadf4k-qzcjyu9e
> https://cp.sync.com/dl/50079a740#dckrc4id-zx548z5k-juh4wzz6-da6zeb9n
> https://cp.sync.com/dl/92d3ba3b0#fqvwe7ii-mc2gckt8-ykmrvfwp-6vhrtzit
> https://cp.sync.com/dl/e55d4bdc0#f5f9ssjr-6mfjiadb-w5zhimcw-xjt7qw5n
>
> > check LIG
> Checking 'LIG'....
> Warning: Close contact of 1.431077 angstroms between .R<LIG 1>.A<C 2> and
> .R<LIG 1>.A<C1 3>

...etc...this is odd: in the mol2 file, it is clear that there are a
lot of missing bonds, which leads Amber to think that these are non-bonded
contacts.

It's not clear to me why this is happening, but I can reproduce the problem.
We'll have to examine this... It looks like it should be something
identifiable in the input pdb file, but I don't see it (so far).

> I ignored the warnings after check LIG. Is it correct?

No: these are very serious warnings: essentially the bonding pattern and atom
types are all wrong.

....dac


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Received on Sun Sep 25 2016 - 14:00:02 PDT