AMBER Archive (2006)

Subject: AMBER: minimization of Hydrogens with xLeaP

From: rebeca_at_mmb.pcb.ub.es
Date: Mon Nov 27 2006 - 12:38:04 CST

Hello,
I am a new user of AMBER and I have a problem with the minimization of the
hydrogens of my protein. After introducing the hydrogens left in a PDB
structure of a protein using xLeap, I tried to minimize these hydrogens fixing
the rest of the atoms. For this, I used this input:

 &cntrl
  imin=1, maxcyc=5000, ncyc=250, ntb=0, igb=0, cut=10, ibelly=1,
  bellymask='@H=',
/

The energy of the minimization is stable, but the hydrogens appear very bad
situated (the angles are not good). Does anybody know what I am doing wrong?

In the output file you can see this:

          -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 11/27/2006 at 11:32:37
  [-O]verwriting output

File Assignments:
| MDIN: minimizado_H.in
| MDOUT: minimizado_H.out
|INPCRD: dimero.crd
| PARM: dimero.top
|RESTRT: minimizado_H.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 58.790
| New format PARM file being parsed.
| Version = 1.000 Date = 11/21/06 Time = 16:48:41
 NATOM = 12849 NTYPES = 14 NBONH = 6389 MBONA = 6604
 NTHETH = 14540 MTHETA = 8958 NPHIH = 27658 MPHIA = 16726
 NHPARM = 0 NPARM = 0 NNB = 71069 NRES = 830
 NBONA = 6604 NTHETA = 8958 NPHIA = 16726 NUMBND = 42
 NUMANG = 94 NPTRA = 40 NATYP = 28 NPHB = 0
 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 999375
| Hollerith 77926
| Integer 6086776
| Max Pairs 4283000
| Max Rstack 178490
| Max Istack 64245
| Total 50264 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals

--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------

General flags:
     imin = 1, nmropt = 0

Nature and format of input:
     ntx = 1, irest = 0, ntrx = 1

Nature and format of output:
     ntxo = 1, ntpr = 50, ntrx = 1, ntwr = 500
     iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
     ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
     ntf = 1, ntb = 0, igb = 0, nsnb = 25
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000

Frozen or restrained atoms:
     ibelly = 1, ntr = 0

Energy minimization:
     maxcyc = 5000, ncyc = 250, ntmin = 1
     dx0 = 0.01000, drms = 0.00010

    LOADING THE BELLY ATOMS AS GROUPS

     Mask @H=; matches 6389 atoms

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 0

     Sum of charges from parm topology file = -17.00000056

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------

     eedmeth=4: Setting switch to one everywhere

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 9.4666E+06 2.8460E+06 2.1751E+08 HB2 9728

 BOND = 14.1126 ANGLE = 948.2155 DIHED = 2096.9435
 VDWAALS = 9861386.5074 EEL = -378253.6396 HBOND = 0.0000
 1-4 VDW = 1213.0223 1-4 EEL = -20797.8943 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
     50 -3.9655E+05 2.4718E+00 2.7487E+02 HB3 3304

 BOND = 74.3346 ANGLE = 994.8820 DIHED = 2054.4274
 VDWAALS = -675.9978 EEL = -379326.3519 HBOND = 0.0000
 1-4 VDW = 1132.2569 1-4 EEL = -20799.6027 RESTRAINT = 0.0000

>From here the energy does not change very much.

Thanks a lot for your help.

Best wishes,

Rebeca García
Postdoctoral student
Parc Cientific de Barcelona
Spain

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