Re: RNA_minimization

From: jrui_at_ci.uc.pt
Date: Tue Feb 26 2008 - 13:45:04 CST

Hi,

Try this:
set 1anr [atomselect top "nucleic and noh"]
$1anr writepdb 1anrn.pdb

See the manual for more on atom selections:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node78.html
http://www.ks.uiuc.edu/Research/vmd/current/ug/node79.html

Also, you are using writepdb and writepsf with the same output file name.

Hope this helps,
Rui Rodrigues

Quoting sripad chandan <sripadchandan_at_gmail.com>:

> hii,
> I am working on RNA protein interaction.
> I have minimized the protein with NAMD after homology modeling.
> (Thanks you all for your kind help. Ramya Narasimhan , Ryon)
> Now I want to minimize the RNA.
> As I am new i followed the basic tutorial for protein.
> I am coming across these difficulties.
>
> 1)*for creating for a pdb file with RNA with out hydrogen i have put*
> set 1anr [atomselect top nucleic]
> $1anr writepdb 1anrn.pdb
>
> *1anr is my RNA molecule.*
> sure it gives an pdb file. but when i checked it still contains hydrogen.
> so should i make some modification?
>
> 2) *I have taken the psfgen file as*
>
> package require psfgen
> topology top_all27_na.rtf
> alias residue A ADE
> alias residue G GUA
> alias residue C CYT
> alias residue U URA
> segment U {
> pdb 1anrn.pdb
> first 5PHO
> last 3TER
> }
> coordpdb 1anrn.pdb U
> guesscoord
> writepdb 1anr.psf
> writepsf 1anr.psf
>
> *which gives (only the last part)*
>
> unknown residue type C
> unknown residue type C
> extracted 29 residues from pdb file
> setting patch for first residue to 5PHO
> setting patch for last residue to 3TER
> Info: generating structure...
> unknown residue type G
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
> *NO PSF file is created. what modification should be done to make it
> correct?*
> **
> 3) *What other modifications should be done in the procedure for minimizing
> and simulating RNA?*
>
>
> Again thanking you for your kind help.
>
> chandan
>
> --
> Sripad Chandan Patnaik
> M.Tech.
> National Institute of Technology, Rourkela
> +91-9861668977
>

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