Can you open up a frame and view it?
On Thu, Jul 25, 2013 at 5:08 PM, Meekyum Olivia Kim <olivijuly.gmail.com>wrote:
> Hello,
>
> I'm trying to do umbrella sampling in implicit solvent with distance
> restraint to calculate the PMF while pulling out the ligand from the
> protein. I'm doing minimization with the adjusted distance between the
> ligand and the receptor center of mass defined in the restraint file,
> without SHAKE, then followed by two equilibration with SHAKE turned on. The
> first equilibration fixes the protein with a small force constant. But the
> first equilibration didn't start and I got this error message regardless of
> the distance between the ligand and protein:
>
>
> | ERROR: I could not understand line 190
> 13.2773028 9.5137563 26.5189041************ 404.8478369************
>
> *s in the inpcrd file often indicate an overflow of the Fortran format used
> to store coordinates in the inpcrd/restart files. This often happens when
> particles diffuse very far away from each other. Make sure you are removing
> center-of-mass translation (nscm /= 0) or check if you have multiple,
> mobile
> molecules that have diffused very far away from each other. This condition
> is
> highly unusual for non-periodic simulations.
>
>
> My equilibration input file looks like:
>
>
> eq1
> &cntrl
> ntr=1, ig=-1, nmropt=1,
> nstlim = 100000, nscm=10,
> cut=30, igb=5, saltcon=0.1,
> ntx=1, irest=0, ntb=0, ntpr=500,
> dt=0.002, nrespa=1,
> ntt=3, tempi=0.0, temp0=300., gamma_ln=2.0,
> ntc=2, ntf=2, tol=0.000001,
> ntwr = 5000, ntwx=5000, ioutfm=1,
> restraintmask=':1-385',
> restraint_wt=5.0
> /
> &wt
> type='END'
> &end
>
> DISANG=restraint
>
>
> And my restraint file is:
>
>
> rst iat=-1,-1, r1=4.6, r2=7.6, r3=7.6, r4=10.6, rk2=200, rk3=200, ialtd=0,
> igr1=440,442,444,447,449,453,457,458,1796,1798,1800,1802,1806,1809,1813,1814,3491,3493,3495,3497,3501,3504,3508,3509,5142,5144,5146,5148,5152,5156,5157,
> igr2=6000,6001,6002,6003,6018,6020
> /
>
>
> where igr1 is for the protein center of mass and igr2 is for the ligand
> center of mass.
> Would anyone give me some solutions? Thank you very much!
>
> Best,
> Olivia
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--
--
Levi Pierce | Senior Software Developer | Schrodinger, Inc. | *(212)548-2379
*
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Received on Thu Jul 25 2013 - 20:30:03 PDT
