I wonder why a box is involved? You extracted your molecule from the box, so why is a box needed?
Bill
<div>-------- Original message --------</div><div>From: Maryam Hamzehee <maryam_h_7860.yahoo.com> </div><div>Date:06/10/2015 2:50 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: [AMBER] problem with extraction of potential energy for the ligand </div><div>
</div>Dear Amber list
I am trying to extract potential energy for my ligand. I successfully generated the trajectory file for my ligand from the trajectory of ligand-receptor complex. I am using sander for getting the potential energy of my ligand during MD simulation but got the following error:
------------------------------------------------------- Amber 11 SANDER 2010 -------------------------------------------------------
| Run on 06/10/2015 at 13:15:13 [-O]verwriting output
File Assignments:| MDIN: lig_en_extract.in | MDOUT: lig_en_extract.out |INPCRD: lig.inpcrd | PARM: lig.prmtop |RESTRT: restrt | REFC: refc | MDVEL: mdvel | MDEN: mden | MDCRD: mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip
|INPTRA: lig_box.traj | Here is the input file: Extracting energy &cntrl imin=5,ntx=1,maxcyc=1 cut=9999.0,ntb=0 ntc=2,ntf=2 ntpr=1,ntwx=1 /
-------------------------------------------------------------------------------- 1. RESOURCE USE: --------------------------------------------------------------------------------
| Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation| *** cutoff > system size, list only builds once|Largest sphere to fit in unit cell has radius = 32.926| New format PARM file being parsed.| Version = 1.000 Date = 06/10/15 Time = 11:25:55 NATOM = 32 NTYPES = 6 NBONH = 10 MBONA = 24 NTHETH = 15 MTHETA = 36 NPHIH = 34 MPHIA = 59 NHPARM = 0 NPARM = 0 NNB = 163 NRES = 1 NBONA = 24 NTHETA = 36 NPHIA = 59 NUMBND = 12 NUMANG = 18 NPTRA = 8 NATYP = 9 NPHB = 0 IFBOX = 0 NMXRS = 32 IFCAP = 0 NEXTRA = 0 NCOPY = 0
| Memory Use Allocated| Real 3224| Hollerith 99| Integer 25463| Max Pairs 496| nblistReal 384| nblist Int 1012662| Total 4085 kbytes
| Note: 1-4 EEL scale factors were NOT found in the topology file.| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.| Using default value of 2.0.| Duplicated 0 dihedrals| Duplicated 0 dihedrals
-------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN--------------------------------------------------------------------------------
QUE
General flags: imin = 5, nmropt = 0
Nature and format of input: ntx = 1, irest = 0, ntrx = 1
Nature and format of output: ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500 iwrap = 0, ntwx = 1, ntwv = 0, ntwe = 0 ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function: ntf = 2, ntb = 0, igb = 0, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut =9999.00000, intdiel = 1.00000
Frozen or restrained atoms: ibelly = 0, ntr = 0
Energy minimization: maxcyc = 1, ncyc = 10, ntmin = 1 dx0 = 0.01000, drms = 0.00010
SHAKE: ntc = 2, jfastw = 0 tol = 0.00001| INFO: Old style inpcrd file read
-------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES--------------------------------------------------------------------------------
QUE begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
Sum of charges from parm topology file = 0.00000000 Forcing neutrality...
-------------------------------------------------------------------------------- 4. RESULTS--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIEStrajectory generated by ptraj minimizing coord set # 1 ---------------------------------------------------
eedmeth=4: Setting switch to one everywhere
---------------------------------------------------| Local SIZE OF NONBOND LIST = 342| TOTAL SIZE OF NONBOND LIST = 342
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER 1 -5.0349E+01 2.2192E+01 6.9293E+01 C16 12
BOND = 7.2942 ANGLE = 12.6678 DIHED = 11.6701 VDWAALS = 5.2658 EEL = 54.7855 HBOND = 0.0000 1-4 VDW = 15.8415 1-4 EEL = -157.8742 RESTRAINT = 0.0000minimization completed, ENE= -.50349304E+02 RMS= 0.221919E+02minimizing coord set # 2 Frac coord min, max: -0.781282269331228 1.34956817325996 The system has extended beyond the extent of the virtual box. Restarting sander will recalculate a new virtual box with 30 Angstroms extra on each side, if there is a restart file for this configuration. SANDER BOMB in subroutine Routine: map_coords (ew_force.f) Atom out of bounds. If a restart has been written, restarting should resolve the error
Any help would be highly appreciated.
Best regardsMaryam
P.S. The out file is also attached.
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Received on Wed Jun 10 2015 - 08:00:02 PDT
