Thank you Dr Ross, I will do both. Hopefully I can get some interesting
results.
On Thu, Jan 21, 2016 at 11:09 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> If the ions are at a periodic boundary, it should not matter if they are
> on one side or both.
>
> If that is the issue, you have two valid trajectories to compare, which
> is good.
>
> Bill
>
> On 1/21/16 8:03 PM, Bin Wang wrote:
> > Dear Amber users,
> >
> > This time the POPS problem is solved. I only used the leaprc.lipid11,
> > lipid11.lib and lipid11.dat files in the xleap, and I don't need to
> change
> > the liipid residue numbers. Now I am running minimization and heating,
> > hopefully it will go well.
> >
> > Now I have another question about the ions because the membrane is a
> > mixture of POPC and POPS. In the Charmm webserver, all of ions were added
> > on the upper side of the membrane, but the lower side also has some POPS
> > molecules. So I deleted all of the Charmm ions and used xleap to add
> ions.
> > This time the ions locate on both sides of the bilayer membrane. In the
> > real experiments, the ions should be on both sides. I am not sure which
> ion
> > distribution I should use. So I am running both structures now.. Could
> > anybody give me some suggestions on this issue?
> >
> > Thank you very much!
> >
> >
> > Bin
> >
> >
> >
> >
> > On Tue, Jan 19, 2016 at 4:26 PM, Benjamin D Madej <bmadej.ucsd.edu>
> wrote:
> >
> >> Hi Bin,
> >>
> >> As Ross just posted, POPS is not supported in the current version of
> >> Lipid14. Supported molecules are listed in the Amber manual. To
> reiterate,
> >> do not mix Lipid14 and Lipid11 parameters.
> >>
> >> As Ross also stated, we have completed parameterization of PS will be
> >> released as an expansion to Lipid14. I am currently preparing the
> >> manuscript for publication and parameters will be released with
> AmberTools
> >> 16.
> >>
> >> lipid14_supp.lib was not meant to be released with Amber 14 and just
> >> includes old topologies and charges from Lipid11. Do not use this file.
> >>
> >> A couple more notes:
> >> 1. Some of the errors regarding POPS were because of the missing
> >> parameters. This is correct because Lipid14 does not have PS parameters.
> >>
> >> 2. A comment about the PDB file residue numbers. According to the PDB
> file
> >> specification (available on the RCSB PDB web site), each residue should
> >> have a unique residue number. The residue numbers are often listed
> >> incrementally increasing for each residue. To clarify, each tail and
> head
> >> group in Lipid14 is technically a PDB file residue. However, for the
> case
> >> of Lipid14 lipids with three residues, unique residue numbers is
> acceptable
> >> but not required for Leap. The following sequence, however is required:
> >>
> >> Lipid 1 sn-1 tail
> >> Lipid 1 head
> >> Lipid 1 sn-2 tail
> >> TER
> >> Lipid 2 sn-1 tail
> >> Lipid 2 head
> >> Lipid 2 sn-2 tail
> >> TER
> >> ...
> >>
> >> I have tested this many times. The charmmlipid2amber.py script does not
> >> alter lipid residue numbers because Leap can automatically split the
> >> residues. Leap will also automatically assign topology and parameters as
> >> well as connect the residues.
> >>
> >> Benjamin Madej
> >> Postdoctoral Scholar
> >> San Diego Supercomputer Center, UC San Diego
> >>
> >> ________________________________________
> >> From: Ross Walker [ross.rosswalker.co.uk]
> >> Sent: Tuesday, January 19, 2016 1:05 PM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] Problem when using lipid14 force filed in Amber 11
> >>
> >> 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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Received on Fri Jan 22 2016 - 18:00:03 PST
