AMBER Archive (2003)

Subject: leap problem

From: yuan bo (yuanbous_at_yahoo.com)
Date: Wed Apr 23 2003 - 22:49:36 CDT

Dear Amber users
I download acntonitrile all-atoms parameters from
amber website and use it to solvate one protein in
xleap of Amber6:
>>frcmod = loadamberparams ch3cn_all.pcy
>>loadAmberPrep ch3cn_all.in
>>solvatebox protein C3N 5 (C3N is variable name of
acetonitrile in ch3cn_all.in file )
 Solute vdw bounding box: 56.888 45.091
46.347
  Total bounding box for atom centers: 66.888 55.091
56.347
  Solvent unit box: 6.214 5.471
4.653
  Total vdw box size: 68.354 49.239
51.183 angstroms.
  Volume: 172265.733 A^3
  Total mass 54772.882 amu, Density 0.528 g/cc
  Added 721 residues
>> saveamberparm protein prmtop inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 671 improper torsions applied
Building H-Bond parameters.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res total affected

        CASN 1
        CSER 1
        CTYR 1
        NALA 1
        NCYX 1
        NILE 1
  )
I don't know why amount of acetonitrile
molecules(e.g."C3N 721" )is not presented after
"saveamberparm" command. Because amount of water could
be showed after "saveamberparm" command when I solvate
protein using TIP3 water model or WATBOX216. But there
are correct amount of residue when I check prmtop
file. however I am still a bit worry if there are some
wrong which could results in uncorrect results of MD.
There are same problem when I solvate protein using
Methanol solvent box from library of Amber6. Could
anybody tell me the reason?
Thanks in advance
yb

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