Hi Cheng,
> I tried to build a starting structure from the protein sequence containing
> 440 residues.
> However, the residues were overloaded in tleap.
> I tried to input the sequence starting from 100, 150, 200 residues and so
> on.
> I could get topology and coordinate files from tleap when inputting 249
> residues.
> When I increased the residues to 250, tleap did work.
> Does AMBER set limitation for the input sequence in tleap?
> For large proteins, what shall I do to get starting files?
This is way beyond what the sequence command was ever designed to do and
trying to fold a 440 residue protein from a straight chain is orders of
magnitude beyond what is even remotely possible with MD. If you don't have
an initial crystal structure I would suggest taking a look into possible
homology modeling programs that will try to predict a starting structure for
you based on similarity to other known protein structures.
Good luck,
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 14 2010 - 23:00:04 PDT
