Dear mailing list,
I have many pdb of the simulation of solute in tip4p waterbox and need
to convert into into prmtop/inpcrd for ptraj to look at watershell.
I wrote script converts atom names of my pdb into amber readable and then writes
leap.in file to create required files and then submits as to tleap
leap-file does:
source leaprc.ff99SB
source leaprc.gaff
loadamberparams frcmod.tip4p
WAT = TP4
loadamberparams /home/matsumoto/aniline.frcmod
loadamberprep /home/matsumoto/aniline.prepi
x = loadpdb ./iteration_0001/0.300000/output_001_0001.pdbptr
saveamberparm x ./iteration_0001/0.300000/output_001_0001.pdbptr.top
./iteration_0001/0.300000/output_001_0001.pdbptr.crd
quit
i get all required files but am concerned about warning:
not concerned of warning atom epw connected to o (as tip4p)
but why is leap log saying :
This is the additional/replacement parameter set for TIP4P
(UNKNOWN ATOM TYPE: EP)
My atoms name H1, H2, O and EPW and resname WAT or TP4, but resname
WAT/TP4 does not change behaviour.
This error common or concern?
Thank you
Aiko
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Received on Fri Nov 26 2010 - 03:30:04 PST
