Atom distance & ptraj

From: bo baker (bo.bybaker_at_gmail.com)
Date: Thu Jan 05 2006 - 11:47:46 CST

• Next message: Dong Luo: "What's the highest temperature I can go?"
• Previous message: Shirley Li: "PSFGEN for protein containing GTP"
• Next in thread: Peter Freddolino: "Re: Atom distance & ptraj"
• Reply: Peter Freddolino: "Re: Atom distance & ptraj"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi,

I try to use 'ptraj' to extract the distance information. There is one
prolem here. How NAMD mask the atoms in the files of .psf and .dcd? I
tried the way as in Amber, but didn't work. Here is how I did:

ptraj N62-2wation.psf < n62namd-dist1.in

test1:

----
trajin N62-2equil1.dcd.gz
distance a1 out N62-2eq1a.dist  time 0.02 :169_at_OE1 :188_at_NH1
strip :WAT
go
----
The error message:
Mask [:169_at_OE1] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:188_at_NH1] represents 0 atoms !!!NO ATOMS DETECTED!!!
Test2:
----
trajin N62-2equil1.dcd.gz
distance a1 out N62-2eq1a.dist  time 0.02 :1661 :1931
strip :WAT
go
-----
The error message:
Mask [:1661] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:1931] represents 0 atoms !!!NO ATOMS DETECTED!!!
Thanks for any advices.
Bo

• Next message: Dong Luo: "What's the highest temperature I can go?"
• Previous message: Shirley Li: "PSFGEN for protein containing GTP"
• Next in thread: Peter Freddolino: "Re: Atom distance & ptraj"
• Reply: Peter Freddolino: "Re: Atom distance & ptraj"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:13 CST