Dear Jason
The problem was fixed according to your suggestion. Many thanks for your help.
All the bestMaryam
On Thursday, 11 June 2015, 1:03, Bill Ross <ross.cgl.ucsf.edu> wrote:
I am not sure how a box is being used - since it is failing on the 2nd coordinate set, maybe there are box coords in the traj file.
Bill
<div>-------- Original message --------</div><div>From: Maryam Hamzehee <maryam_h_7860.yahoo.com> </div><div>Date:06/10/2015 10:45 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 Bill
Many thanks for the email. When I produce the lig.traj (trajectory of the ligand) using "no box" option, sander gives error message saying that it can't read the box from the mdcrd file. That's why we used the box. How we can ignore the box?
ThanksMaryam
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
I wonder why a box is involved? You extracted your molecule from the box, so why is a box needed?
Bill
-------- Original message --------From: Maryam HamzeheeDate:06/10/2015 2:50 AM (GMT-08:00)To: AMBER Mailing ListSubject: [AMBER] problem with extraction of potential energy for the ligand
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 Thu Jun 11 2015 - 05:00:03 PDT
