Dear Amber user,
I need to put a restraint on just part of my proteins during the production
step. My system is the slice of Nucleosome ( the mixture of DNA and histone
protein), first I created the PDB file from my topology and coordinate
files by "ambpdb", from this PDB files I found the residue number which I
wanted to be free (residue 111 to 134). I tried different methods for
applying restraint (below), but none of them worked. I checked "mdout" file
the restrained energy in all of the cases is zero.
=========================================
Hold the DNA fixed
10
RES 169 201
END
RESTRAIN ALL
10
RES 1 110
RES 135 168
END
END
==========================================
RESTRAIN ALL
10
RES 1 110
RES 135 201
END
END
=================================
"mdout"
================================
NSTEP = 250000 TIME(PS) = 1270.000 TEMP(K) = 301.54 PRESS =
32.4
Etot = -378784.3942 EKtot = 63190.7188 EPtot =
-441975.1130
BOND = 951.3362 ANGLE = 2191.6176 DIHED =
2407.7612
1-4 NB = 883.0099 1-4 EEL = 2086.4980 VDWAALS =
57161.1723
EELEC = -507656.5081 EHBOND = 0.0000 *RESTRAINT = 0.0000*
EKCMT = 30991.5326 VIRIAL = 30263.1781 VOLUME =
1042152.6042 Density
= 1.0169
==================================================
any idea what is wrong?
--
Parviz Seifpanahi
Ph.D. Candidate
Department of Physics
Virgina Tech, Blacksburg, Va 24061
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Received on Sun Aug 27 2017 - 08:30:03 PDT
