AMBER Archive (2009)

Subject: [AMBER] QM/MM input file error

From: mahesh kumar (kumar.kumarmahesh.mahesh74_at_gmail.com)
Date: Thu Dec 03 2009 - 08:05:25 CST

HI
I am working on protein molecular to which i docked my ligand. I want to do
QM/MM calculations on this docked molecule.
I wants residue number 7,38,45,210 to be studied by QM. so i give qmmask
line in this way as given in tutorial but it is not working properly.
*
qmmask=':7,38,45,210' *
but in output file , it shows matches 2101 atoms which is not correct. total
number of atoms for 7,38,45,210 residue is 87.
so i tried with another option.
*iqmatoms
*but in the manual it is written that you have to specify atoms numbers from
prmtop file. i had check whole prmtop file but it doesnot have information
about the atom numbers.
So please kindly advice me for problem.
thank you in advance
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber