Dear mailing list,
I have many pdb of the simulation of solute in tip4p waterbox and need
to convert into into prmtop/inpcrd
as useing ptraj to look at watershell. 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 tleap -s -f scipt
leap-file does:
source leaprc.ff99SB
source leaprc.gaff
loadamberparams frcmod.tip4p
WAT = TP4
loadamberparams /home/patrick/aniline.frcmod
loadamberprep /home/patrick/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.
You please help?
Thank you
Aiko
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Received on Wed Nov 24 2010 - 16:30:04 PST
