Hi Thomas,
>From the end of tutorial B1:
http://ambermd.org/tutorials/basic/tutorial1/section6.htm
trajin a-dna_md2.mdcrd.gz
trajin a-dna_md3.mdcrd.gz
trajin a-dna_md4.mdcrd.gz
trajin a-dna_md5.mdcrd.gz
trajin a-dna_md6.mdcrd.gz
trajin a-dna_md7.mdcrd.gz
trajin a-dna_md8.mdcrd.gz
trajin a-dna_md9.mdcrd.gz
trajin a-dna_md10.mdcrd.gz
average a-dna_20-1820ps_average.pdb pdb nowrap
In your case you would start by splitting your pdb file into multiple
copies, one for each structure then just change the mdcrd files for pdb
files (ptraj should recognize them):
trajin 1.pdb
trajin 2.pdb
trajin 3.pdb
...
...
...
average average.pdb pdb nowrap
Note this assumes you have a prmtop file for one of the pdbs and the
topologies are identical. You could also try VMD - it will load a multi
structure pdb as a series of frames in a trajectory and then it may have a
tool to average them - although I have never actually tried it.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Lake, Thomas
> Sent: Thursday, January 22, 2009 5:44 AM
> To: amber.ambermd.org
> Subject: [AMBER] (no subject)
>
> I am trying to generate an average PDB structure, from a PDB containing
> multiple structures. I think I need to use ptraj to do this, but am not
> sure what to write in the input file. Can anyone help.
>
> Thanks
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 23 2009 - 01:21:55 PST
