No, with chainA_MOL alone gave same problems. I am taking a drastically
different strategy.
francesco
On Sat, Dec 20, 2014 at 5:23 PM, Francesco Pietra <chiendarret.gmail.com>
wrote:
> 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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>
>
>
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Received on Sat Dec 20 2014 - 12:00:02 PST
