Dear AMBER user
I want to minimize structure in TIP3PBOX in two state (min1.in and min2.in
|| input files below).
In particular I want to minimize my molecule where zinc coordinated atoms
(SG of CYS and NE2 of HIS and ZN of Zinc) in the restrained or freeze mode
so that I can save my metal geometry. min1.in runs fine but for min2.in
there is an error with ntr=1. Im not able to launch minimization. it says
rfec file is missing or not readable. Im using amber 12.
I used following style or definition to restrain single atom in 4 different
residues instead of all the atom in the single residue.
min2.in
.
.
.
.
Group input for restrained atoms
500.0
RES 4.SG, 7.SG, 19.NE2, 22.NE2, 26.ZN
so I am not sure is it correct way to define just to restrain single atom
in 4 different residues as 4.SG, 7.SG, 19.NE2, 22.NE2, 26.ZN
if any one know to restrain single atom please suggest me
thanks in advance
Vince
PS : the files that I using to minimization
min1.in
=========
Peptide : minimisation solvent+ions with molecule fided
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntb = 1,
ntr = 1,
cut = 10.0,
ntpr = 50,
ntwx = 50
/
Hold Peptide_solvate fixed
500.0
RES 1 26
END
END
min2.in
========
Peptide : minimisation entire system
&cntrl
imin = 1,
maxcyc = 2500,
ncyc = 1000,
ntb = 1,
ntr = 1,
cut = 10.0,
ntpr = 50,
ntwx = 50
/
Group input for restrained atoms
500.0
RES 4.SG, 7.SG, 19.NE2, 22.NE2, 26.ZN
END
END
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 09 2016 - 14:00:03 PDT
