Thank you Dr. Walker and Dr. Madej, I will change the leapin file.
Hopefully this problem can be solved soon. And thank you for being patient
to me.
Bin
On Tue, Jan 19, 2016 at 4:05 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Bin,
>
> Ah - I read this better now - sorry I was reading POPC rather than POPS.
>
> POPS is not supported in lipid14. It was in lipid11 and can be used with
> the rest of lipid11 with a constant surface tension term. It should not be
> mixed with lipid14 parameters. POPS support will be released as an update
> to lipid14 - we are waiting on publication. Current plan is to include it
> as part of AmberTools16.
>
> Do NOT use lipid14_supp.lib it is dubious origin (basically a holding
> place for lipid11 parameters that were to be reparameterized in line with
> lipid14). It should never have been included in the released version of
> AmberTools.
>
> Sorry for the confusion.
>
> Either way do NOT load lipid14.dat and then lipid11.dat - this will over
> write all sorts of parameters and you'll get a weird mix. Lipid 11 and
> lipid 14 should not be considered to be mixable.
>
> All the best
> Ross
>
> > On Jan 19, 2016, at 12:11 PM, Bin Wang <ben.wangbj.gmail.com> wrote:
> >
> > 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
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
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> >>
> >>
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Received on Tue Jan 19 2016 - 14:00:03 PST
