On Thu, 2015-05-07 at 18:15 +0430, Fatemeh Sadat Alavi wrote:
> Hi all users
> I use sander to conduct a short minimization, I do my minimization in two
> steps and I have successfully minimized!
> I can see box's information in output file:
> NATOM = 49755 NTYPES = 18 NBONH = 47961 MBONA = 1833
> NTHETH = 4028 MTHETA = 2484 NPHIH = 8017 MPHIA = 6084
> NHPARM = 0 NPARM = 0 NNB = 81261 NRES = 15617
> NBONA = 1833 NTHETA = 2484 NPHIA = 6084 NUMBND = 52
> NUMANG = 112 NPTRA = 52 NATYP = 33 NPHB = 1
> IFBOX = 2 NMXRS = 73 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
>
> | Memory Use Allocated
> | Real 3169401
> | Hollerith 164884
> | Integer 1840083
> | Max Pairs 28658880
> | nblistReal 597060
> | nblist Int 1676292
> | Total 155754 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: TRUNCATED OCTAHEDRON
> The second step is the heating of the system from 0 to 300 K, this step does
> completely but there aren't any box's information in output file!
>
> 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 = 36.357
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/04/15 Time = 18:36:49
> NATOM = 49755 NTYPES = 18 NBONH = 47961 MBONA = 1833
> NTHETH = 4028 MTHETA = 2484 NPHIH = 8017 MPHIA = 6084
> NHPARM = 0 NPARM = 0 NNB = 81261 NRES = 15617
> NBONA = 1833 NTHETA = 2484 NPHIA = 6084 NUMBND = 52
> NUMANG = 112 NPTRA = 52 NATYP = 33 NPHB = 1
> IFBOX = 0 NMXRS = 73 IFCAP = 0 NEXTRA = 0
> NCOPY = 0
>
> my input file was :
> heat complex
>
> &cntrl
>
> imin=0,irest=0,ntx=1,
>
> nstlim=25000,dt=0.002,
>
> ntc=2,ntf=2,
>
> cut=8.0, ntb=1,
>
> ntpr=100, ntwx=100,
>
> ntt=3, gamma_ln=2.0,
>
> tempi=0.0, temp0=300.0,
>
> ntr=1,
>
> restraintmask = ':!(:WAT) & !(:Cl-) & !(:Na+)' ! keep solutes fixed,
>
> restraint_wt=2.0,
>
> nmropt=1
>
> /
>
> &wt TYPE='TEMP0', istep1=0, istep2=25000,
>
> value1=0.1, value2=300.0, /
>
> &wt TYPE='END' /
>
>
> for next step, I need box's information and I have this error:
> (NTB /= 0 && NTP /= 0) but IFBOX == 0
>
> This combination is not supported
>
> Can you help me? please give your valuable comments.
> Thanks in advance.
Did you modify your prmtop file at all? Are you using the same prmtop
file for each simulation? I've never seen this happen before.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 07 2015 - 07:30:04 PDT
