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

[Mark Abraham]

On 4/20/2011 3:49 PM, Liao Chuan wrote:
>
> HI, Itamer and Mark, thanks for your prompt replies.
>
> Pymol, Amber and Sybyl are commercial software. Any free
> software/scripts?
>

There's a reason I said AmberTools. Google is your friend.

Mark

> - Chuan
>
> ------------------------------------------------------------------------
>
> *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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