Dear Dian,
> Maybe I should not call it peptide in the first place. It is a fairly big
> molecule (>250 atoms) with some parts resemble amino acids like Glu, Gln,
> Ser, Arg etc. That's why I treated it as a big ligand. How would you
> parameterize a molecule like this in Amber? Could you kindly take a look at
> my pdb file? Many thanks.
You need to:
- load the Amber Force Field Topology Database (FFTopDB) to look at
which amino-acid residues are already available (i.e. the .off or .lib
files).
- check the peptide bonds in your peptide: do you really want cis
peptide bonds
- check the charged groups of your amino-acids in your peptide: for
instance, do you really want a COOH group instead of COO(-); at pH 7
the carboxylate group is present
- among the amino-acid residues in your peptide isolate these that are
not in the Amber FFTopDB: you will need to generate a new force field
library for these modified/unknown residues (check in the literature
if your modified/unknown residue is not already known/parameterized;
search in the Amber and R.E.DD.B. databases as well).
Then to learn how to create the central, N-terminal & C-terminal
fragments for a modified/unknown residue, read:
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
See also tutorials at q4md-forcefieldtools.org
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
regards, Francois
> On Tue, Jan 31, 2012 at 1:06 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Dian Jiao,
>>
>> You should look at the output of the semi-empirical tool used
>> (divcon/mopac/sqm/...): It looks like the job failed... My
>> understanding is that a job performed with a semi-empirical method
>> should be fast (in particular, if the optimization threshold is loose).
>>
>> You reported "pep.pdb": does it mean an entire peptide is involved in
>> the computation? in general, one wants to generate a new force field
>> library only for a modified residue; the regular residues are handled
>> by the Amber Force Filed Topology DataBase...
>>
>> regards, Francois
>>
>>
>> > I was trying to model this peptide with the following command:
>> >
>> > antechamber -i pep.pdb -fi pdb -o pep.mol2 -fo mol2 -c bcc.
>> >
>> > After about 24 hours, the job "finished" except that it didn't generate
>> > pep.mol2 file. All other output files seem okay, including
>> > ANTECHAMBER_BOND_TYPE.AC0, ANTECHAMBER_AM1BCC_PRE.AC, sqm.in and
>> sqm.out.
>> > So what happened to mol2? Was the file written to somewhere else?
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Received on Tue Jan 31 2012 - 22:30:02 PST
