Dear All,
I want to strip large number of residues (which are waters, > more than 20K that are not required).
As this link (suggested by Prof. Cheatham
http://archive.ambermd.org/201110/0216.html) says "since after each strip the
residue numbers are re-ordered", I wrote a simple script to re-number the residues and do stripping one by one. But I think after each strip file is read again so it is taking long time to complete. May be it will take hours and I have many such files to be stripped.
So I tried to strip just in single step so that ptraj reads file once only (same link
http://archive.ambermd.org/201110/0216.html), but I end with an error in ptraj.out
(please see attached file as the
format cannot be retained here in mail due to ugly nature of ptraj.in as single line has large number of residues, ptraj.in and ptraj.out)
Doing this helps me in two ways : no need to re-number residues (correct me if wrong) and its faster
error is like RPN/n which I believe is limit of ptraj to read one line and it expects to be on second line?
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- application/octet-stream attachment: ptraj.in
- application/octet-stream attachment: ptraj.out
Received on Sun Jul 22 2012 - 03:00:02 PDT
