Dear Amber friends
I am willing to simulate 20mer peptide implicitly in lipid
environment using GBSA method. I tried to simulate the peptide with EXTDIEL
= 4. Unfortunately i could not find the EXDIEL value in my output file. With
this mail i attached the output file of my simulation. Therefore i would
like to know how to simulate the peptide in lipid environment implicitly.
Kindly help me in this regard. Eagerly waiting for your reply
Dynamics out file details
-------------------------------------------------------
Amber 9 SANDER 2006
-------------------------------------------------------
| Run on 02/05/2008 at 22:53:47
[-O]verwriting output
File Assignments:
| MDIN:
../dyn.in
| MDOUT: 1.dyn.out
|INPCRD: 1.min.rst
| PARM: 1.top
|RESTRT: 1.dyn.rst
| REFC:
refc
| MDVEL:
mdvel
| MDEN: 1.mden
| MDCRD: 1.mdcrd
|MDINFO:
mdinfo
|INPDIP:
inpdip
|RSTDIP:
rstdip
Here is the input file:
dynamics of peptide
implicit
&cntrl
IMIN =
0,
NTX =
1,
NTPR =
100,
NTWR =
100,
NTWX =
100,
NTWE =
100,
NTR =
0,
NSTLIM=
5000000,
NTT =
3,
DT = 0.002,
TEMP0 = 300.0,
TEMPI = 300.0,
GAMMA_LN =
2,
NTP =
0,
NTC =
2,
NTF =
2,
NTB =
0,
IGB =
5,
CUT =
15,
RGBMAX =
15,
GBSA =
0,
EXTDIEL =
4,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
MPI
| New format PARM file being parsed.
| Version = 1.000 Date = 01/15/08 Time = 18:01:13
NATOM = 432 NTYPES = 11 NBONH = 221 MBONA = 218
NTHETH = 497 MTHETA = 290 NPHIH = 920 MPHIA = 695
NHPARM = 0 NPARM = 0 NNB = 2352 NRES = 27
NBONA = 218 NTHETA = 290 NPHIA = 695 NUMBND = 33
NUMANG = 69 NPTRA = 37 NATYP = 22 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii
(mbondi)
| Memory Use Allocated
| Real 24044
| Hollerith 2621
| Integer 42189
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 362 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ACE
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 100, ntrx = 1, ntwr =
100
iwrap = 0, ntwx = 100, ntwv = 0, ntwe =
100
ioutfm = 0, ntwprt = 0, idecomp = 0,
rbornstat= 0
Potential function:
ntf = 2, ntb = 0, igb = 5, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 15.00000, intdiel = 1.00000
saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000
gbbeta = 0.80000, gbgamma = 4.85100, surften = 0.00500
rdt = 0.00000, rgbmax = 15.00000
alpb = 0
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 5000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 300.00000, gamma_ln= 2.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACE
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
| Atom division among processors:
| 0 77 115 173 229 275 337 385
| 432
| Running AMBER/MPI version on 8 nodes
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 356.93 PRESS =
0.0
Etot = -189.1922 EKtot = 381.2408 EPtot = -
570.4330
BOND = 16.9437 ANGLE = 97.9319 DIHED =
166.5203
1-4 NB = 68.9903 1-4 EEL = 866.9065 VDWAALS = -
83.3495
EELEC = -1263.9145 EGB = -440.4618 RESTRAINT =
0.0000
------------------------------------------------------------------------------
--
S.Sundar Raman
Chemical Lab,
CLRI
Chennai-20
ph: 044-24411830
-----------------------------------------------------------------------
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Received on Sun Feb 10 2008 - 06:07:04 PST
