Dear Amber users:
I am having problems to equilibrate a pure Protein-Membrane system using amber. The system contains 252,817 atoms in total. The minimization and the heating parts (NVT ensemble) are performed without any error.
When I started the equilibration under NPT ensemble, the system started expanding until it crashes. I first used semi-isotropic conditions without surface tension as suggested in the files generated in CHARMM-GUI/amber folder and then anisotropic conditions as suggested in the Lipid 14 Tutorial 16 and in some threads from amber mailing list. Both of them did the same.
I used CHARMM-GUI to build my membrane made of pure POPC lipids. Then I followed AMBER Tutorial 16 and the README file generated in the amber folder of CHARMM-GUI to prepare all my files for minimization, equilibration and production.
I converted the lipids format from CHARMM to AMBER using the chamberlipid2amber.py script. I also used the vmd_box_dims.sh script to determine the periodic box dimension. Each residue after this conversion (PA-PC-OL) is represented by only one residue, but when I used LEaP (AMBER 14, lipid14, FF14SB, Ambertools 15) to generate the parameter files, each residue is split in 3 resides (PA, PC and OL). Based on what I read from the amber mailing list and understood, this is expected. My concern is about the TER card after each part of the lipid residue. LEaP introduces a TER card after each tail and head phospholipid, that is:
PA 1 (tail)
TER
PC 2 (head)
TER
OL 3 (tail)
TER
In Lipid 14/Tutorial 16 and in some of the threads from the amber mailing list I found that the format should be as below (that is only one TER card after each lipid):
Lipid 1 sn-1 tailte
Lipid 1 head
Lipid 1 sn-2 tail
TER
Lipid 2 sn-1 tail
Lipid 2 head
Lipid 2 sn-2 tail
TER
My questions are:
1) Is the TER card between each lipid's members OKAY? I mean:
PA 1 (tail)
TER
PC 2 (head)
TER
OL 3 (tail)
TER
Or it could be like the output from LEaP in AMBER 14 and 16:
PA 1 (tail)
PC 2 (head)
OL 3 (tail)
TER
2) Could you please give me any suggestion on why the membrane is expanding from initial rectangular periodic box dimensions of
126.0299988 126.3920021 170.8379974 (Intial Structure) to
146.2263471 143.1649336 182.6060295 (after 25 ps at NPT ensemble conditions)?
I also used the vmd_box_dims.sh script to determine the initial periodic box dimension after the conversion from CHAEM to AMBER.
Thanks very much in advance.
Best,
Yoel Rodriguez, PhD
The City University of New York
Mount Sinai School of Medicine
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Received on Thu Oct 13 2016 - 14:00:02 PDT
