Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
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 terrence...@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 liaoch...@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-boun...@gromacs.org [mailto:gmx-users-boun...@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
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Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
There is another free tool (Avogadro) which is pretty easy to handle this also. Try http://avogadro.openmolecules.net/wiki/Get_Avogadro in Build -- Inert --- Peptides, Which is very easy to use. you can choose Straight line, beta sheet or alpha helix or other. and save as .pdb lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
apt-get install avogadro http://avogadro.openmolecules.net/wiki/Distribution_Packages On Wed, Apr 20, 2011 at 10:34 PM, ZHAO Lina lnzha...@gmail.com wrote: There is another free tool (Avogadro) which is pretty easy to handle this also. Try http://avogadro.openmolecules.net/wiki/Get_Avogadro in Build -- Inert --- Peptides, Which is very easy to use. you can choose Straight line, beta sheet or alpha helix or other. and save as .pdb lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
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-boun...@gromacs.org [mailto:gmx-users-boun...@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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
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-boun...@gromacs.org [mailto:gmx-users-boun...@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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?
Hi Chuan, Leap is a part of Ambertools which is free. See http://ambermd.org/#AmberTools Good luck. Terry 2011/4/20 Liao Chuan liaoch...@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-boun...@gromacs.org [mailto:gmx-users-boun...@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 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
