Dear Ross,
I want to do a checkoverlap of my protein-ligand complex. Apparently
there is a problem with the structure (although I don;t really
understand why, since I minimized the complex in MOE before loading it
into leap, in order to get rid of bad contacts). Using the swiss pdb
viewer, I can see some close contacts, but nothing really bad (in my
opinon).
I set up the ptraj checkoverlap friday, using my mdcrd file from xleap,
and it has been calculating since.
Unfortunately I cannot attach the file to the list, so I will go ahead
and send it to you separately.
Thanks for your reply,
Carsten
Ross Walker wrote:
> Dear Carsten,
>
> What are you wanting ptraj to do? Process an mdcrd file? And if so, how many
> frames.
>
> A simple rms fit to the initial structure for 4,600 atoms x 1,000 frames
> should take less than a minute on a 3GHz P4.
>
> Please be more specific - include your input file with the email if you can.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
>
>
>>-----Original Message-----
>>From: owner-amber.scripps.edu
>>[mailto:owner-amber.scripps.edu] On Behalf Of Carsten Detering
>>Sent: 01 March 2004 09:23
>>To: amber.scripps.edu
>>Subject: AMBER: ptraj
>>
>>Hello Ambers,
>>
>>I would like to know how long I should expect a ptraj
>>calculation (4600
>>atoms, noimage) to last approximately. I use a dual Xeon with
>>4Gbyte memory.
>>
>>thanks in advance,
>>
>>Carsten
>>
>>
>>--
>>
>>Carsten Detering
>>University of Washington
>>Seattle, WA 98195
>>Fon 206.543.5081
>>Fax 206.685.8665
>>
>>
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>>The AMBER Mail Reflector
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>>
>
>
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--
--------------------------------------------------------------
Carsten Detering | detering.u.washington.edu
University of Washington |
Department of Chemistry | Fon +1.206.543.5081
Box 351700 | Fax +1.206.685.8665
Seattle, WA 98195-1700 |
USA |
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Received on Tue Mar 02 2004 - 18:53:01 PST
