AMBER Archive (2008)

Subject: AMBER: Query related to implicit solvent EXTDIEL

From: S.Sundar Raman (sundar02_at_gmail.com)
Date: Wed Feb 06 2008 - 06:03:02 CST

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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