AMBER Archive (2008)

Subject: AMBER: ptraj: new mask parser

From: Vlad Cojocaru (
Date: Wed Jan 23 2008 - 05:59:24 CST

Dear amber users,

I was trying tu use the following mask string in ptraj (the version
distributed with AMBER 9)

":1-466 & !@H="

to select the heavy atoms of a protein. According to the AMBER 9 manual
this should work if enclosed in double quotes (which I did). However I
always get an error saying "the = symbol wasnt recognized"

The "=" symbol is described in the manual as an accepted mask wildcard
in the new mask parser.

Could somebody tell me why is this happening? Is there a bug that I am
not aware of ?



Dr. Vlad Cojocaru

EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg

Tel: ++49-6221-533266 Fax: ++49-6221-533298


---------------------------------------------------------------------------- EML Research gGmbH Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter ----------------------------------------------------------------------------

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to