Re: [AMBER] peptideligandParameters

From: FyD <>
Date: Sat, 25 Oct 2014 07:17:11 +0200

Dear zayan alhalabi,

It looks like you need to generate molecular fragments; your could use
R.E.D. Server Dev./PyRED at
See Tutorials:

You could look at the F-85 project in REDDB:

N,N-dimethylsuccinamide and various protective groups are handled... I
guess you could use a similar approach...

regards, Francois

> I would like to ask you about the parameters for
> peptide ,my peptide has a small modification
> :3,3-dimethyle-succinyle-lysine peptide and also it has benzoyl
> chemical group in the c- terminal ... how can I generate the
> parameters for this peptide befor doing MD with the protein. and
> when I tried to generate parameters in antechamber and then x-leap ,
> the x-leap always give me wrong charges and missing parameters for
> many atoms .

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Received on Fri Oct 24 2014 - 22:30:02 PDT
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