RE: Θέμα: Re: [gmx-users] cyclic peptides

[Mu Yuguang (Dr)]

If I am not wrong, what you want to do is to build a topological file correctly for a cyclic peptide.
You can do this:
For example, your peptide has 5 (n=5) aa: CAAAD,
You can build easily a linear topology file for a six (n+1) aa peptide chain ( with -ter  switch answered by none): CAAADC, the last one should be the same as the first one.
Then you can change the atom number for the last AA to the number for the first aa by just substracting the total number for the 5 AA from the atom number larger than that.


Best regards
Yuguang
 
Dr. Yuguang Mu
Assistant Professor
School of Biological Sciences
Nanyang Technological University
60 Nanyang Drive  Singapore 637551 Tel: +65-63162885 Fax: +65-67913856
http://genome.sbs.ntu.edu.sg/Staff/YGMu/index.php
 

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
Sent: Thursday, August 17, 2006 10:51 PM
To: Discussion list for GROMACS users
Subject: Re: Θέμα: Re: [gmx-users] cyclic peptides

Efi Mantzourani wrote:
> Hi David,
> 
> had a look for the specbond entry, but apparently it is for creating a 
> bond between ligand and receptor. I don't have that. Mine is not a 
> special bond. it is just that pdb2gmx tries to find a terminus for all 
> the chains.

just try it anyway. you may have to sepcify the specific residue type of 
the N-terminus and C-terminus.

> 
> */David van der Spoel <spoel at xray.bmc.uu.se>/* έγραψε:
> 
>     Efi Mantzourani wrote:
>      > Hi all,
>      >
>      > I am trying to run a gromacs trajectory on a ligand-receptor
>     complex,
>      > where the ligand is a head-to-tail cyclic peptide. I add the -ter
>     option
>      > in the pdb2gmx command, so that i can turn off the charged
>     termini in
>      > the peptide. Unfortunately, it will only work keeping the N
>     terminus as
>      > -NH2 (meaning it will add two hydrogens on the resulting
>     structure) or
>      > as N (in this case it doesn't add any hydrogens). They are both
>     wrong,
>      > as I want one hydrogen, like in a normal peptide bond. If i try to
>      > change the resulting files manually its a pain! The gro file is easy
>      > enough, but the topology file has to be altered so that the added
>      > hydrogen is in the correct atom and residue serial number. That
>     means i
>      > have to change all the remaining atoms, all angles, dihedrals
>     etc. Its
>      > just impossible as my complex has about 3.000 atoms! Any
>     suggestions???
> 
>     try making a specbond entry, you have to make sure that the coordinates
>     are OK. please report back if succesfull.
>      >
>      >
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>     David.
>     ________________________________________________________________________
>     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>     Dept. of Cell and Molecular Biology, Uppsala University.
>     Husargatan 3, Box 596, 75124 Uppsala, Sweden
>     phone: 46 18 471 4205 fax: 46 18 511 755
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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