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 - 11:30:03 PST
