Dear Amber users/developers:
I am trying to run a LIE calculation on sander by setting
ilrt = 1
ilrtmask = ':408'
but the i get the following error:
SANDER BOMB in subroutine setup in linear_response.f
an atom type occurs both in solvent and solute
(see complete output below)
Can anyone help me with this issue? I was advised to run LIE (LRT) in sander because my ligand has an extra-point and MM-PBSA does not recognize extra-points.
Thanks in advance
Emilio
-------------------------------------------------------
Amber 12 SANDER 2012
-------------------------------------------------------
| Run on 03/30/2015 at 16:42:41
[-O]verwriting output
File Assignments:
| MDIN: lie.in
| MDOUT: lie.out
|INPCRD: ../md_10.rst
| PARM: ../D2h_halo-Br.top
|RESTRT: ../lie.rst
| REFC: ../md_10.rst
| MDVEL: mdvel
| MDEN: mden
| MDCRD: lie.crd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
5000 ps heating to 300 K restraints backbone
&cntrl
imin=0, irest=1, ntx=5,
ntt=3, temp0=300, gamma_ln=5.0,
cut=10, ntf=2, ntc=2, ntb=2, ntp=1,
nstlim=500000, dt=0.002, tautp=2.0,
ntpr=1000, ntwx=1000, ntwr=1000,
ntr=1, restraint_wt = 1.0,
ilrt = 1,
lrtmask = ':408'
restraintmask = ':4-25.CA|:32-60.CA|:68-101.CA|:113-138.CA|:330-361.CA|:369-3
/
&ewald
nfft1=50, nfft2=50, nfft3=50,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 33.496
| New format PARM file being parsed.
| Version = 1.000 Date = 11/14/14 Time = 15:21:01
NATOM = 72229 NTYPES = 19 NBONH = 68931 MBONA = 3354
NTHETH = 7704 MTHETA = 4562 NPHIH = 14854 MPHIA = 11506
NHPARM = 0 NPARM = 0 NNB = 124445 NRES = 22275
NBONA = 3354 NTHETA = 4562 NPHIA = 11506 NUMBND = 62
NUMANG = 119 NPTRA = 46 NATYP = 46 NPHB = 1
IFBOX = 1 NMXRS = 47 IFCAP = 0 NEXTRA = 1
NCOPY = 0
| Memory Use Allocated
| Real 4345601
| Hollerith 238964
| Integer 2952904
| Max Pairs 49924684
| nblistReal 866748
| nblist Int 2634289
| Total 258498 kbytes
| Note: 1-4 EEL scale factors are being read from the topology file.
| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
BOX TYPE: RECTILINEAR
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1000, ntrx = 1, ntwr = 1000
iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 1
restraint_wt = 1.00000
Molecular dynamics:
nstlim = 500000, nscm = 0, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 5.00000
Pressure regulation:
ntp = 1
pres0 = 1.00000, comp = 44.60000, taup = 1.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
Extra-points options:
frameon = 1, chngmask= 1
Linear Response Theory: ilrt = 1 lrt_interval = 50
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 66.992 Box Y = 95.023 Box Z = 114.028
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 50 NFFT2 = 50 NFFT3 = 50
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
defa
Mask :4-25.CA|:32-60.CA|:68-101.CA|:113-138.CA|:330-361.CA|:369-393.CA; matches 168 atoms
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 68931 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 68931 0
| EXTRA_PTS, trim_bonds: num bonds BEFORE trim = 3354 0
| EXTRA_PTS, trim_bonds: num bonds AFTER trim = 3353 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 7704 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 7704 0
| EXTRA_PTS, trim_theta: num angle BEFORE trim = 4562 0
| EXTRA_PTS, trim_theta: num angle AFTER trim = 4562 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 14854 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 14854 0
| EXTRA_PTS, trim_phi: num diheds BEFORE trim = 11506 0
| EXTRA_PTS, trim_phi: num diheds AFTER trim = 11506 0
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 10500.000 ps
Number of triangulated 3-point waters found: 21842
Sum of charges from parm topology file = -0.00000417
Forcing neutrality...
Setting up LRT calculation
LRT Mask :408; matches 47 atoms
SANDER BOMB in subroutine setup in linear_response.f
an atom type occurs both in solvent and solute
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Received on Mon Mar 30 2015 - 13:30:10 PDT
