Using abmer16/AmberTools17 (under Ubuntu 16.04), I encounter a problem
which is illustrated in amber tutorial A16 (using lipid forcefields).
That tutorial recommends using the on-line CHARMM-GUI site to build
lipid bilayers, with or without embedded protein. And shows how to
convert charmm-gui output pdb's into xleap compatible input. In my
hands, the first part of the tutorial -- involving just lipids,
water,ions -- works fine.
The second part of the tutorial suggests embedding rhodopsin in such a
lipid bilayer. The final "part5_assembly.pdb" returned by charmm-gui
looks reasonable (e.g. in vnd), but after loading the file ("loadpdb")
the file into xleap, when attempting to "saveAmberParm", I get a slew of
fatal errors, like those below. I get such an error message for every
atom in the protein part of the assembly (but no errors relevant to
non-protein atoms.)
******************************************************************
FATAL: Atom .R<CALA 348>.A<HN 12> does not have a type.
FATAL: Atom .R<CALA 348>.A<OT1 13> does not have a type.
FATAL: Atom .R<CALA 348>.A<OT2 14> does not have a type.
Failed to generate parameters
Parameter file was not saved.
***************************************************************
I've tried lots of things to diagnose the problem: Excerpting just the
protein parts of the charmm-gui-pdb-file results in the same errors.
Using the original rhodopsin file ("1u19.pdb" in xleap succeeds, and
generates the prmtop and inpcrd files. Noticing that the
charmm-gui-pdb's do not have a column-78-element name (as specified in
the pdb file protocol), I manually added these -- but to no avail; xleap
still returns the same fatal errors. The A16 tutorial calls for sourcing
leaprc.lipid14 and leaprc.ff12SB; I have also tried sourcing
leaprc.protein.ff14SB.
I pasted below is the last part of the protein-atoms entries in the
charmm-gui-pdb file. (Cloumnation not clear; "PROA" ends at column 76.)
**************************************************************
ATOM 5460 C ALA 348 -9.211 -1.173 -36.862 1.00 0.00 PROA
ATOM 5461 OT1 ALA 348 -10.021 -0.363 -36.336 1.00 0.00 PROA
ATOM 5462 OT2 ALA 348 -9.323 -1.620 -38.035 1.00 0.00 PROA
TER
END
*************************************************************
Any hints, suggestions, remedies will be much appreciated.
Bob Wohlhueter
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Received on Mon Jul 10 2017 - 10:00:03 PDT
