I was unable to get either the metal complex, MOL. top crd, or the whole
metalloprotein, PROT.top crd, saved even by removing bond commands between
MOL and PROT from the script for leap, setting the bond commands once the
script was raised.
As I previously succeeded with a similar (though simples, just one metal
and protein single chain), I wonder whether leap gets confused (or required
a different layout) by the presence of several chains in this new protein,
X.pdb.
>From the leap log:
> PROT = loadpdb X.pdb
Loading PDB file: ./X.pdb
Enter zPdbReadScan from call depth 0.
(starting new molecule for chain B)
(starting new molecule for chain C)
(starting new molecule for chain E)
(starting new molecule for chain X)
(starting new molecule for chain A)
(starting new molecule for chain B)
(starting new molecule for chain C)
(starting new molecule for chain E)
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA
X is for MOL.
A is the protein chain containing MOL as last residue before waters.
These "starting" lines were not present in previous simples case, and are
the only difference I can notice between the two log files. No errors, no
"Warning" that is not followed by "ignoring the waring".
francesco
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret.gmail.com>
Date: Fri, Dec 19, 2014 at 9:55 PM
Subject: Re: [AMBER] unclear leap crashing
To: AMBER Mailing List <amber.ambermd.org>
Can you say more about "crashes"? There don't seem to be any error
> messages.
> Is there any other indication at the terminal about what happened?
>
With crash I meant that leap halts where I showed, with zero byte
.parm7/.rst7. Nothing on terminal more than on log. I am trying different
leap and frcmod options, particularly as to
set MOL head /tail/connect
and
bond unit ... (of MOL to unit)
I also tried to rename atom type N* -> NN throughout, at no avail.
There is something - might well be trivial - that escapes my attention.
Hope to come here soon with more specific questions, if not the solution.
thanks
francesco
On Fri, Dec 19, 2014 at 2:05 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Thu, Dec 18, 2014, Francesco Pietra wrote:
>
> > However, leap crashes after loading the impropers of MOL.
>
> Can you say more about "crashes"? There don't seem to be any error
> messages.
> Is there any other indication at the terminal about what happened?
>
> >
> > To the extent that it might be relevant, notice that even though leap
> does
> > not complain any more about atom type N* in the syntax "N*", impropers
> > involving "N*" were not built.
>
> LEaP only builds impropers if there are corresponding entries in the loaded
> parameter sets. Double check that this is the case (assuming you want
> those
> impropers).
>
> >
> > I wonder whether N* should be rewritten as "N*" also in the frcmod file,
> > other that (as I did) in the script to leap, for example ipropers
>
> No.
>
> ....dac
>
>
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Received on Sat Dec 20 2014 - 08:30:02 PST
