AMBER Archive (2009)

Subject: RE: [AMBER] Do I need to modify the cap residues

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Apr 06 2009 - 23:59:37 CDT

Hi David,

> You still din't tell me how to add caped residues in my
>existing PDB. I have tried in the following way but am not sure if it is
the
>right way.
>> mol = loadpdb my.pdb
>>mol = sequence {ACE mol NME}
        
>Please let me know if it is the right way to add caped residues. If it is
>not then how do I add. Thanx in advance.

I see no reason why this wouldn't work. Do you get any error message when
you try this? The only thing you might find is that the structure is
strained so you might want to select the two capping residues and relax them
in the edit window. You might want to have it create a new unit as part of
the sequence command so you can undo things. I.e. mol2 = sequence ...

Alternatively you can modify your pdb file to include the capping residues.
E.g. see the following thread: http://archive.ambermd.org/200706/0418.html

All the best
Ross

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|\oss Walker

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| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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