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

[Tsjerk Wassenaar]

Hi,

Pymol is sort of semi commercial. You can install it easily on Ubuntu,
using apt-get install pymol (free!), you can install from source (also
free!). You can obtain an educational build (also free!, though
requiring registration). Any will do for the building of sequences,
which on linux is as simple as running:

for i in Y W F A; do for j in Y W F A; do for k in Y W F A; do for l
in Y W F A; do
PEP=H$i$j$k$lPAS
pymol -qcd "editor.build_peptide('${PEP}');cmd.save('$PEP.pdb')"
done; done; done; done

Hope it helps,

Tsjerk


2011/4/20 Terry <terrencesun at gmail.com>:
>
> Hi Chuan,
> Leap is a part of Ambertools which is free.
> See http://ambermd.org/#AmberTools
> Good luck.
> Terry
>
> 2011/4/20 Liao Chuan <liaochuan at tju.edu.cn>
>>
>> HI, Itamer and Mark, thanks for your prompt replies.
>>
>> Pymol, Amber and Sybyl are commercial software. Any free software/scripts?
>>
>>
>>
>> - 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands