I don't happen to have moil-view installed. Is there
another way to do this with simple amber commands?
Eric
--- Peter Gannett <pgannett_at_hsc.wvu.edu> wrote:
> Eric:
>
> I am certainly not the expert on this. However, I
> have run into this problem. Average structures from
> an MD run are just that and can lead to the weird
> things you mention and others - like flat
> deoxyribose rings. Rather than an average
> structure, perhaps a 'most representative structure'
> would suit your needs better. This can be obtained
> using the cluster analysis option of Moil-View.
>
> Hope this helps.
>
> Pete Gannett
>
>
> >>> eric hu <erichu_linux_at_yahoo.com> 01/21/03
> 01:53PM >>>
> Hi, I use carnal to generate an average pdb file
> from
> the trajectory. It seems to me that the new
> structure
> looks a little bit weird. Some C-H bonds are
> extremely
> short while C-N bonds are ridiculous large. These
> happen on both the substrate and the protein. I
> wonder
> if people ever run into the similar situation. By
> the
> way I use antechamber to generate the force
> parameter
> for my substrate.
>
> Eric
>
>
> # carnal.in--generate average pdb file
> FILES_IN
> PARM p1 ./4bound.top;
> STREAM s1 ./TS4_md2.mdcrd.gz;
> FILES_OUT
> COORD c1 ./TS4_1ns.pdb PDB;
> DECLARE
> OUTPUT
> COORD c1 s1 AVERAGE;
> END
>
>
> __________________________________________________
> Do you Yahoo!?
> Yahoo! Mail Plus - Powerful. Affordable. Sign up
> now.
> http://mailplus.yahoo.com
>
>
__________________________________________________
Do you Yahoo!?
Yahoo! Mail Plus - Powerful. Affordable. Sign up now.
http://mailplus.yahoo.com
Received on Tue Jan 21 2003 - 13:02:34 PST
