Dear esteemed Amber Users,
I am new to amber but i found it very efficient and its really a user
friendly simulation program, nevertheless I aim to first equilbrate my
ternary lipids for fungal membranes that is (POPC:POPE:ERG) ERG ==
Ergosterol and the model sytems is fully built from charmm-Gui plat
form. However, to use these lipids i have to covert them to amber
readable format by the t/xleap program but the conversion tool does not
describe atom types for ergosterol, I am Using the charmm2amber.py
script but i get errors when loading the PDB file and also i cannot form
the prmtop and incrd files for simulation with sander/pmemd.
The lipids of choice with respect to Ergosterol seem not to be described
into the charmm2amber.py script thus the atom types, charges and other
parameters for this specific are not defined in this specific file but
the other lipids used (POPE and POPC) are fully described. I tried to
deal with the ergosterol separating it form the rest of the lipids so as
i define its topologies using its force fields from charmm that can be
translated in amber but still topologies in the tleap program could not
be formed for this specific lipid as well as the entire system as a
whole when combined. I also tried entechamber but it was only limited to
1000 atoms in a molecule and ergosterol atoms were above the required
number. Could there be any remedy of such an issue in amber please like
how to modified the charmm2amber.py script so as it could recognize and
convert the atom types for ergosterol please.
Lutimba Stuart, Msc.
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Received on Mon Jun 17 2019 - 12:30:02 PDT
