Dr. Walker, Dr. Case, and Jean-Marc,
Thank you all for your kindly help. This time I add all .lib and .dat files
I can find in the leapin, and it works. It is shown below.
source leaprc.lipid14
source leaprc.lipid11
source leaprc.ff12SB
loadoff /opt/amber14/dat/leap/lib/lipid11.lib
loadoff /opt/amber14/dat/leap/lib/lipid14.lib
loadoff /opt/amber14/dat/leap/lib/lipid14_supp.lib
loadamberparams frcmod.ionsjc_tip3p
loadamberparams /opt/amber14/dat/leap/parm/lipid14.dat
loadamberparams /opt/amber14/dat/leap/parm/lipid11.dat
m = loadpdb membrane.pdb
I do need to read the manual more carefully.
I guess I got all of these format problems because I use the charged lipid
molecule POPS?
On Tue, Jan 19, 2016 at 12:05 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Jan 19, 2016, Bin Wang wrote:
>
> > > > The leapin file I used is shown below:
> > > > source leaprc.lipid14
> > > > source leaprc.ff12SB
> > > > loadoff /opt/amber14/dat/leap/lib/lipid14_supp.lib
> > > > loadamberparams frcmod.ionsjc_tip3p
> > > > m = loadpdb membrane.pdb
>
> You need to look carefully for errors in the first line. Just type
> "tleap -f leaprc.lipid14" and look carefully for any error messages you
> might get. Or, examine the leap.log file you have from the above, find
> the lines that run loadamberparams on lipid14.dat, and look for any errors
> there.
>
> [Developers: we should consider the pros and cons of having errors in
> loading
> files be fatal -- that way the corresponding error messages would be less
> likely to missed. Downside is that some existing scripts will start to
> fail...may be some other downsides as well.]
>
> ....dac
>
>
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Received on Tue Jan 19 2016 - 11:00:04 PST
