AMBER Archive (2002)

Subject: Questions about xleap and mm_pbsa]

From: Salinthip Thipayang (salinthip.thipayang_at_ic.ac.uk)
Date: Fri Jul 19 2002 - 12:49:08 CDT

> Dear amber users,
>
> I am trying to change an amino acid residue in the active site of a protein
> and calculate the binding free energies using MM-PBSA in amber 6. I have run
> minimization, heating and equilibrium MD using SANDER with PME and waterbox
> 216. The mdcrd file was used in the MM-PBSA run for the native protein.
>
> The next step is to modify GLU in the active site to GLN and then compare the
> binding free energies.
>
> I am thinking of the following approaches.
>
> 1) Create the PDB file from the restart file obtained from the MD run using
> CARNAL
> 2) in XLEAP, loadpdb and then change the GLU264 to GLN 264
> 3) run belly MD first only allow the GLN264 to move and fix other residues and
> water and then run another belly MD allowing all the residues to move except
> the ligand so that the ligand can find the optimal structure with all the
> residues.
> 4) then run full MD for the whole system.
>
> However, in the 2nd step in XLEAP I encountered this problem of XLEAP deleting
> some of the water molecule when i replace GLU with GLN. GLN has more atoms
> that GLU and so when replace GLU with GLN there are some overlap atom numbers
> in the PDB file.
>
> XLEAP gives the following message
>
> > mutant2 = loadpdb "./mutantGLN_b4_xleap2.pdb"
> Loading PDB file: ./mutantGLN_b4_xleap2.pdb
> -- residue 10240: duplicate H1 atoms (total 10)
> -- residue 10240: duplicate H2 atoms (total 10)
> -- residue 10240: duplicate O atoms (total 10)
> -- residue 10496: duplicate H1 atoms (total 10)
> -- residue 10496: duplicate H2 atoms (total 10)
> -- residue 10496: duplicate O atoms (total 10)
> -- residue 10752: duplicate H1 atoms (total 10)
> -- residue 10752: duplicate H2 atoms (total 10)
> -- residue 10752: duplicate O atoms (total 10)
> -- residue 11008: duplicate H1 atoms (total 10)
> -- residue 11008: duplicate H2 atoms (total 10)
> -- residue 11008: duplicate O atoms (total 10)
> -- residue 11264: duplicate H1 atoms (total 10)
> -- residue 11264: duplicate H2 atoms (total 10)
>
> and so on...
>
> ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
> (same-name atoms are reduced to a single atom)
>
> total atoms in file: 96182
>
> Is there any way to modify the PDB file without ruin all the atom numbers and
> prevent water molecules getting deleted?
>
> I understand that there is Alanine-Glysine scaning option in MM-PBSA that i
> could use and would preventing me from having to do all the above 3 steps but
> this is only to change from CH3 to H not -OH to -NH2 as i would like to do
> with GLU to GLN. Is this a reasonable approach? Is there any other way of
> doing the mutation? Any comments and suggestions will be very appreciated.
>
> Thank you very much.
>
> Sally
>
>
>
>
> --
> -------------------------------------------------------------------------------
> Salinthip Thipayang (Miss)
>
> PhD Research Student
> Biological and Biophysical Chemistry Research Group
> Chemistry Department
> Imperial College of Science, Technology and Medicine
> Exhibition Road
> London SW7 2AY
> The United Kingdom
> Tel: +44(0)207 5945851
> Fax: +44(0)207 5945845
> Email: salinthip.thipayang_at_ic.ac.uk
> --------------------------------------------------------------------------------
>
>

am