Hello Jason,
Thank you very much for your reply. I removed the : infront of the ., but it showed error:
Warning: cannot find template for residue ARG in our library.
You will not be able to save prmtop for this molecule.
Warning: cannot find template for residue CYX in our library.
You will not be able to save prmtop for this molecule.
Warning: cannot find template for residue CYX in our library.
You will not be able to save prmtop for this molecule.
Warning: cannot find template for residue CYX in our library.
You will not be able to save prmtop for this molecule.
Warning: cannot find template for residue CYX in our library.
You will not be able to save prmtop for this molecule.
Warning: cannot find template for residue CYX in our library.
You will not be able to save prmtop for this molecule.
Warning: cannot find template for residue CYX in our library.
You will not be able to save prmtop for this molecule.
Warning: there is an atom OXT in residue PHE205 which does not exist in the model PHE!
This atom will not be created.
residue PHE205 has 21 atoms
N
H
CA
HA
CB
HB2
HB3
CG
CD1
HD1
CE1
HE1
CZ
HZ
CE2
HE2
CD2
HD2
C
O
OXT
model PHE has 20 atoms.
N
H
CA
HA
CB
HB2
HB3
CG
CD1
HD1
CE1
HE1
CZ
HZ
CE2
HE2
CD2
HD2
C
O
Warning: cannot find template for residue PHE in our library.
You will not be able to save prmtop for this molecule.
[gtkleap]$ saveAmberParm sys ligand.prmtop _AnteMMPBSA_ligand.rst7
[gtkleap]$ quit
I checked the AnteMMPBSA_ligand.pdb and AnteMMPBSA_receptor.pdb, they are not the right structures. So do you think I should check these residues in the original PDB file?
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: bin wang <wang_p_z.yahoo.com.cn>; AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, November 22, 2011 7:07 AM
Subject: Re: [AMBER] How to use strip mask and receptor mask in the new mmpbsa.py?
Try removing the : in front of the ..
However, ante-MMPBSA.py is fairly limited in its usefulness and applicability in this release. It generates an frcmod and OFF file from the main topology file and tries to create the topology files for the other systems via sleap.
The way it's implemented, it cannot recognize any dimer systems (anything with a charged amino acid terminus in the middle of the protein sequence), and it's dependent on how sleap creates topology files.
The next version will use a far more sophisticated approach that does not involve passing through leap -- it will modify the topology directly and only keep the parameters for the remaining atoms.
HTH,
Jason
--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Nov 21, 2011, at 9:40 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Dear Amber users,
> I recently re-compiled AT15 and amber11, then realized the mmpbsa.py is upgraded. However, I cannot figure out how to use the receptor mask. For example, in this command:
> ante-MMPBSA.py -p apt2loop13_solvated.prmtop -c apt2loop13_solvated.inpcrd -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -strip_mask ":WAT:Na+" -receptor_mask ":.1-5099"
>
>
> The receptor should include atoms 1 to 5099, but it didn't work. What should be the right mask? I am looking forward to your help.
> Thank you very much.
>
> Best,
> Bin
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Nov 29 2011 - 13:00:03 PST
