[gmx-users] Re: Structure preparation for the simulation

Itamar Kass itamar.kass at monash.edu
Mon Oct 31 23:42:51 CET 2011

Hi James,

I usually use Swiss-PdbViewer (http://spdbv.vital-it.ch/disclaim.html). Despite being an old and not well supported for any system, it is still a free and easy to use and allows the building and mutating of residues  in addition to automatically adding missing atoms. 

You can just build an extra GLY at the end of the your chain and using text editor change it to N/C-caps.


On 31/10/2011, at 11:16 PM, Dr. Vitaly V. Chaban wrote:

>> Dear Gromacs Users!
>> I'd like to know about external software wich could be used for structure
>> processing for the futher simulation in Gromacs. Today I've tried one of the
>> most popular such software Amber tools but I've forced with problems during
>> compilation of it ") So I'm looking for possible analogues )
>> First of all I'm intresting in software for the addition different CAPing
>> groups to N and C termi of my protein.
>> Is there any plugins for Pymol or VMD for such purposes? I've loked for this
>> option in both of that software but couldnot  find
>> Thank you for your help,
>> James
> Among free solutions... maybe this would help:
> http://www.chemaxon.com/marvin/sketch/index.php
> I don't know molecular editor plugins for VMD, but it would be cool,
> if one is accessible.
> -- 
> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
> Univ. Rochester, Rochester, New York 14627-0216
> --
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"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
| Tel: +61 3 9902 9376
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| E-mail:  Itamar.Kass at monash.edu

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