Dear Amber developers,
I have equilibrated and sampled a protein+lipid bilayer (POPC) system by
maintaining 0.1 M KCl concentration for 80ns using explicit solvent model
with Amber12 and ff99SB + lipid11 forcefields. The N-terminus (residues
1-19) of the protein is anchored into the lipid bilayer. I have reimaged
the system using ptraj for every 10 ns. Upon inspecting the reimaged pdb
file in the VMD, I have observed that the majority of the K+ and Cl- ions
have formed crystals (in the form of FCC lattice). Starting from a few
crystal (smaller in size), by the end of 80ns of simulation the K+ Cl- ions
have aggregated to form a larger crystal. Is this a forcefield effect due
to ff99SB or Lipid11?
The simulation protocol is briefly explained here:
1. Minimized for 10000 steps by constraining the protein
2. Minimized for 10000 steps without any constrians
3. Heated for 20 ns (0-100K) under NVT conditions by constraining the
protein
4. Heated for 100 ns(100-300K) under NPT conditions by constraining the
protein
5. Equilibrated for 25 ns (300K) under NPT conditions by constraining the
protein
6. Sampled for 55 ns (300K) under NPT conditions with a constant surface
tension on the lipid bilayer.
The 3D structure of the protein was generated using homology modeling. The
protein was deforming after the heating process. Hence, the protein was
constrained during the equilibration process.
Due to the above mentioned problem (i.e. crystallization of K+ Cl- ions), I
have generated a pdb file (using ptraj) of the system using the last ns of
the sampling process. Then, stripped all the K+ and Cl- ions from the
reimaged pdb file. Now, I am trying to make a new prmtop and inpcrd files.
However, I am unable to save the topology files with tleap. As I am
getting the following error
Just showing the last part of the error:
Joining PA - PC
Joining PC - OL
Created a new atom named: RH10 within residue: .R<OL 1491>
Created a new atom named: RH11 within residue: .R<OL 1491>
Created a new atom named: SH11 within residue: .R<OL 1491>
Created a new atom named: RH12 within residue: .R<OL 1491>
Created a new atom named: SH12 within residue: .R<OL 1491>
Created a new atom named: RH13 within residue: .R<OL 1491>
Created a new atom named: SH13 within residue: .R<OL 1491>
Created a new atom named: RH14 within residue: .R<OL 1491>
Created a new atom named: SH14 within residue: .R<OL 1491>
Created a new atom named: RH15 within residue: .R<OL 1491>
Created a new atom named: SH15 within residue: .R<OL 1491>
Created a new atom named: RH16 within residue: .R<OL 1491>
Created a new atom named: SH16 within residue: .R<OL 1491>
Created a new atom named: RH17 within residue: .R<OL 1491>
Created a new atom named: SH17 within residue: .R<OL 1491>
Created a new atom named: RH18 within residue: .R<OL 1491>
Created a new atom named: SH18 within residue: .R<OL 1491>
Created a new atom named: TH18 within residue: .R<OL 1491>
Created a new atom named: RH16 within residue: .R<PA 1492>
Created a new atom named: SH16 within residue: .R<PA 1492>
Created a new atom named: TH16 within residue: .R<PA 1492>
Created a new atom named: RH15 within residue: .R<PA 1492>
Created a new atom named: SH15 within residue: .R<PA 1492>
Created a new atom named: RH14 within residue: .R<PA 1492>
Created a new atom named: SH14 within residue: .R<PA 1492>
Created a new atom named: RH13 within residue: .R<PA 1492>
Created a new atom named: SH13 within residue: .R<PA 1492>
Created a new atom named: RH12 within residue: .R<PA 1492>
Created a new atom named: SH12 within residue: .R<PA 1492>
Created a new atom named: RH11 within residue: .R<PA 1492>
Created a new atom named: SH11 within residue: .R<PA 1492>
Created a new atom named: RH10 within residue: .R<PA 1492>
Created a new atom named: SH10 within residue: .R<PA 1492>
Joining PA - PC
Joining PC - OL
Created a new atom named: RH10 within residue: .R<OL 1494>
Created a new atom named: RH11 within residue: .R<OL 1494>
Created a new atom named: SH11 within residue: .R<OL 1494>
Created a new atom named: RH12 within residue: .R<OL 1494>
Created a new atom named: SH12 within residue: .R<OL 1494>
Created a new atom named: RH13 within residue: .R<OL 1494>
Created a new atom named: SH13 within residue: .R<OL 1494>
Created a new atom named: RH14 within residue: .R<OL 1494>
Created a new atom named: SH14 within residue: .R<OL 1494>
Created a new atom named: RH15 within residue: .R<OL 1494>
Created a new atom named: SH15 within residue: .R<OL 1494>
Created a new atom named: RH16 within residue: .R<OL 1494>
Created a new atom named: SH16 within residue: .R<OL 1494>
Created a new atom named: RH17 within residue: .R<OL 1494>
Created a new atom named: SH17 within residue: .R<OL 1494>
Created a new atom named: RH18 within residue: .R<OL 1494>
Created a new atom named: SH18 within residue: .R<OL 1494>
Created a new atom named: TH18 within residue: .R<OL 1494>
total atoms in file: 180861
Leap added 12507 missing atoms according to residue templates:
12507 H / lone pairs
The file contained 12507 atoms not in residue templates
Since added/missing = extra, there is a high probability
of atoms with 'incorrect' names; you may want to
use addPdbAtomMap to map these names, or change in file
Please let me know how to generate the new topology files. I am trying
to further sample the system without counter ions under NPT conditions. Is
there any other way to resolve this issue?
Thanks,
mani
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Received on Fri Jul 05 2013 - 17:30:03 PDT
