答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

[Liao Chuan]

HI, Itamer and Mark, thanks for your prompt replies.

Pymol, Amber and Sybyl are commercial software. Any free software/scripts? 

 

- Chuan

 

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发件人: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
代表 Mark Abraham
发送时间: 2011年4月20日 13:31
收件人: Discussion list for GROMACS users
主题: Re: [gmx-users] any software which could convert a polypeptidesequence
to a pdb file?

 

On 4/20/2011 2:36 PM, Liao Chuan wrote: 

Dear gmx-users,

I want to conduct simulations of a protein and its ligand, a heptapeptide
HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine.
Thus, I will have to conduct a total number of 4*4*4=64 runs. I’ve got the
pdb file of the protein, but I have no idea how to prepare the pdb files of
those 64 heptapeptides with sequences already known. Is there any
software/script which could convert a polypeptide sequence to a pdb file?
Any comment is appreciated!


Leap in the AmberTools package is good for this.

Mark

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