Hi Ross:
Thanks for the advice. Please, see below.
On Thu, Oct 20, 2011 at 9:13 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Francesco,
>
> You might be better posting this question to the NAMD mailing list.
The Giambasu-Case directions - albeit restricted to cpu only - seemed
to invite to talk with amber, too. Sorry for the intrusion following
my misunderstanding.
However
> the following error would appear to be telling:
>
>> FATAL ERROR: Num of atoms in coordinate file is different from that in
>> parm file!
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: Num of atoms in coordinate file is different from
>> that in parm file!
>
> Did you try the CPU only version?
I should install it but I'll take another route as am not interested
in the cpu-only version.
>Does it give the same error? - Have you
> manually checked your prmtop and coordinate files to make sure the atom
> counts match?
I'll do. I assumed that the files provided with the tutorial are
correct. On the other hand, they load correctly to VMD. Better, I'll
run myself xleap for a rectangular box. Curiously, xleap is not in my
installation of amber11/ambertools1.5, while it is in the installation
of amber10.
>
> On another note why not just use GPU AMBER (PMEMD)?
Present status of the Country, with drastic budgetary cuts, have
forced us to priorities. I still am at amber10/ambertools1.5. More
importantly, what i want to simulate can't be done with current
amber11.
>It is significantly
> faster than the NAMD GPU version, especially on GTX580s where it screams!
> and avoids all the complexities, and potential bugs or inaccuracies in
> converting AMBER input files to NAMD.
I wish one day I'll have the possibility to try it.
cheers, and thanks again
francesco
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
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Received on Thu Oct 20 2011 - 01:30:03 PDT
