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
>>>>
>>>>
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>>>>
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Received on Tue Jan 19 2016 - 13:30:05 PST
