[AMBER] free energy calculation and leap error

From: Sadaf Rani <sadafrani6.gmail.com>
Date: Tue, 22 Oct 2019 17:03:04 +0100

Dear Amber users
I am trying to reproduce the ala1 oligomer example for running free energy
calculation as mentioned in https://pubs.acs.org/doi/pdf/10.1021/jp409693p:-
Initially, I build my system by setting 'ACE ALA NME ' sequence in xleap
and generated library and saved topology and parameter file (ala.parm7 and
ala.rst7), run a short MD.
The problem occurs when I take the last coordinate from MD (press.rst7) and
initial topology (ala.parm7) to build the system as follows:-

parm ala.parm7
trajin press.rst7
#stripping ACE ALA NME (alanine and capping residues and saving rest of
strip ":1,2,3"
outtraj solvated.pdb onlyframes 1
# extract the alanine and capping residues
strip ":1-999999"
outtraj ala2_2.pdb onlyframes 1


$tleap -f - <<_EOF
source leaprc.protein.ff03.r1
source leaprc.gaff
source leaprc.water.tip3p
loadAmberParams frcmod.ionsjc_tip3p
loadoff diala.lib
# coordinates for solvated ligands as created previously by MD
ala = loadpdb ala2_2.pdb
lsolv= loadpdb water_only.pdb

# decharge transformation
ala = combine {ala lsolv}
setbox ala vdw
savepdb ala ala2_2_decharge.pdb
saveamberparm ala ala2_2_decharge.parm7 ala2_2_decharge.rst7


I get following leap output:-
Loading library: ./diala.lib
Loading PDB file: ./ala2_2.pdb
Warning: name change in pdb file residue 3 ;
 this residue is split into ALA and NME.
1 residues had naming warnings.
 There are split residues;
 residue sequence numbers will not correspond to those in the pdb.
  Added missing heavy atom: .R<ALA 3>.A<CA 3>
  Added missing heavy atom: .R<ALA 3>.A<CB 5>
  Added missing heavy atom: .R<ALA 3>.A<C 9>
  Added missing heavy atom: .R<ALA 3>.A<O 10>
  Added missing heavy atom: .R<NME 4>.A<N 1>
  total atoms in file: 22
  Leap added 10 missing atoms according to residue templates:
       5 Heavy
       5 H / lone pairs
Loading PDB file: ./water_only.pdb
  total atoms in file: 1146
Box dimensions: 28.016300 30.921600 27.150600
Writing pdb file: ala2_2_decharge.pdb
   printing CRYST1 record to PDB file with box info
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 6 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

res total affected

WAT 382
 (no restraints)

In resulting pdb file I have 32 residues in output pdb file

Could you please suggest me where I am doing mistake?

Thank you
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Received on Tue Oct 22 2019 - 09:30:03 PDT
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