Dear amber users
I am running a 10ns MD with pmemd.MPI.
Since i wanted to restrain 2 distances (protein-ligand distances), I used a distance restr file obtained using makeDIST_RST.
The MD input file is:
&cntrl
imin=0,
irest=1,
ig=-1,
ntx=7,
ntb=2,
ntp=1,
taup=2.0,
igb=0,
ntr=0, nmropt=1,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=1.0,
ntc=2,
ntf=2,
cut=12.0,
nstlim=5000000, dt=0.002,
ntpr=500, ntwx=500, ntwr=1000
/
&wt type='END' /
LISTOUT=POUT
DISANG= RST.dist
Where RST.dist is:
#
# 83 GLU O 247 D6A N6 4.0
&rst
ixpk= 0, nxpk= 0, iat=1273,3839, r1= 1.30, r2= 1.80, r3= 4.00, r4= 4.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
&end
#
# 85 VAL N 247 D6A N1 4.0
&rst
ixpk= 0, nxpk= 0, iat=1295,3840, r1= 1.30, r2= 1.80, r3= 4.00, r4= 4.50, &end
Then I analyzed the output file.
In the output file is written:
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 505.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
** No weight changes given **
RESTRAINTS:
Requested file redirections:
LISTOUT = POUT
DISANG = RST.dist
Restraints will be read from file: RST.dist
Here are comments from the DISANG input file:
#
# 83 GLU O 247 D6A N6 4.0
Number of restraints read = 2
Done reading weight changes/NMR restraints
Number of triangulated 3-point waters found: 8190
Sum of charges from parm topology file = 0.00099988
Forcing neutrality...
| Dynamic Memory, Types Used:
| Reals 2399203
| Integers 1188455
| Nonbonded Pairs Initial Allocation: 1102140
| Running AMBER/MPI version on 32 nodes
Thus, restraints are read from the RST.dist file.
But at each step I got this message:
NSTEP = 64000 TIME(PS) = 633.000 TEMP(K) = 301.40 PRESS = 140.5
Etot = -68685.3858 EKtot = 17601.5660 EPtot = -86286.9518
BOND = 759.0329 ANGLE = 2074.7195 DIHED = 2572.5908
1-4 NB = 912.0684 1-4 EEL = 8829.6357 VDWAALS = 9464.7219
EELEC = -110899.7210 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 7327.9249 VIRIAL = 6471.9218 VOLUME = 282215.6694
Density = 1.0292
Ewald error estimate: 0.1064E-03
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
Should not be Bond = something diverse from 0.000 (since I am using distance constraints) ? Is amber not take into account the distance restraints?
Can someone help me to understand what is happening?
Cheers
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
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Received on Wed Jul 02 2014 - 07:00:02 PDT
