AMBER Archive (2005)

Subject: Re: AMBER: nmode with ibelly

From: Martin Sippel (masi_at_nmr.mpibpc.mpg.de)
Date: Wed Jun 08 2005 - 12:48:04 CDT

('binary' encoding is not supported, stored as-is) Dear Dr Case,

thank you very much for your answer. Using ptraj's strip option, I get polypeptides without proper termini (missing OXT) due
to truncation of adjacent amino acids; xleap sets the missing termini of the chosen residues automatically, so I get different
numbers of atoms in my trajectory (obtained with ptraj) and the prmtop-file, hence sander and nmode give error messages.
Should I convert all my snapshots from the trajectory to inpcrd-files that come along with the prmtop-files in xleap to get
starting structures for the minimisation/entropy calculations? Or what should I do?

Best regards,

Martin

>>
>> ...with ibelly = 1 option the entropy calculation doesn't work
>> (there ist this message: "Thermo analysis not supported for belly calc.") ?!
>> How can I define that only certrain residues should be considered for the
>> entropy calculation to speed it up?
>>
>
>You would have to create a prmtop file with just the "important" residues, and
>use ptraj to strip away the unwanted parts of the system. Then run what is
>left through nmode.
>
>You could also enable the printing of thermodynamic information when belly is
>enabled, but be sure to think carefully about what the results mean.
>
>...dac
>
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