Dear all,
I am trying to run an MD simulation of my tetrameric protein while heating from 0 to 300K, applying positional restraints for some residues and distance restraints for other residues but the job stops.
Here I report the input file:
Stage 3 heating 0 to 300K with distance restraints on Fe4S4 - CYS
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10.0,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
ig = -1,
gamma_ln = 1.0,
nstlim = 500000, dt = 0.002,
ntpr = 100, ntwx = 100, ntwr = 1000
nmropt = 1
&end
/
&wt
type = 'DUMPFREQ', istep1 = 50
/
DISANG = LAMPLP_RST.dist
DUMPAVE = LAMPLP_dist.dat /
&wt type = 'END'
/
Hold SAM and PLP
50.0
RES 1641 1642
END
Hold SAM and PLP
50.0
RES 1645 1646
END
Hold SAM and PLP
50.0
RES 1649 1650
END
Hold SAM and PLP
50.0
RES 1653 1654
END
END
While the output ends with:
5. REFERENCE ATOM COORDINATES
default_name
----- READING GROUP 1; TITLE:
Hold
GROUP 1 HAS HARMONIC CONSTRAINTS 50.00000
GRP 1 RES 1641 TO 1642
Number of atoms in this group = 94
----- READING GROUP 2; TITLE:
Hold
GROUP 2 HAS HARMONIC CONSTRAINTS 50.00000
GRP 2 RES 1645 TO 1646
Number of atoms in this group = 94
----- READING GROUP 3; TITLE:
Hold
GROUP 3 HAS HARMONIC CONSTRAINTS 50.00000
GRP 3 RES 1649 TO 1650
Number of atoms in this group = 94
----- READING GROUP 4; TITLE:
Hold
GROUP 4 HAS HARMONIC CONSTRAINTS 50.00000
GRP 4 RES 1653 TO 1654
Number of atoms in this group = 94
----- READING GROUP 5; TITLE:
END
GROUP 5 HAS HARMONIC CONSTRAINTS 0.00000
rfree: End of file on unit 5
I found on the manual that should be the way apply pos. restraints to different groups of molecules, but it looks like can't read the distance restraints and is looking for other GROUP to read instead.
I am trying to run it using pmemd on a GPU with Amber14.
Is there anything am I doing wrong that I cannot see?
Any help would be appreciated.
Damiano
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Received on Wed Apr 13 2016 - 07:00:03 PDT
