Dr. Walker,
I did followed each step exactly in that tutorial, and unfortunately it did
not work in my case from the conversion of format using that
charmmlipid2amber.py program. The PS was not recognized in Amber. No TER
was added after each WAT and K+ ion. Then Jean-Marc helped me added the
lipid14_supp.lib and changed residue numbers of all lipids. But I still had
pdb format problem. Then I correct all of the pdb format problem, and I
still got the "Could not find bond parameter" problem. In short, this is
how I spent several weeks and cannot find why the tutorial is not working.
So far, I still think the problem is from one of the .dat or .lib file.
charmmlipid2amber.py
On Tue, Jan 19, 2016 at 2:06 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> UGH!!!!
>
> No do NOT do this - who knows what crazy frankenstein combination of
> parameters you will get doing something like this. :-(
>
> Please work through the following tutorial:
> http://ambermd.org/tutorials/advanced/tutorial16/
>
> And follow each step exactly and see if this works. If it does not then it
> suggests something is messed up with your AMBER installation.
>
> All the best
> Ross
>
> > On Jan 19, 2016, at 10:40 AM, Bin Wang <ben.wangbj.gmail.com> wrote:
> >
> > 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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> >>
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>
>
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Received on Tue Jan 19 2016 - 12:30:03 PST
