Just as a general note from my own personal experience combining Charmm parameter files for use with Chamber. You must be absolutely sure that there are no duplicate entries in the file (for example multiple entries from TIP3P which often appears in each parameter file from Charmm). Chamber will parse things and then set force constants and reference distances to zero for some other bond or angle unrelated to the duplicate without issuing any sort of error or warning. It is well worth your time to go back and check the prmtop files that Chamber produces to be sure this hasn't happened.
Best of luck,
Josh
On Apr 3, 2012, at 4:47 PM, Crowley, Michael wrote:
> Albert,
> I took this off line to not crowd the amber list with these details.
> Mike
>
> --
> Michael F. Crowley, Ph.D.
> Principal Scientist, Biomolecular Sciences Division
> National Renewable Energy Laboratory
> 1617 Cole Blvd.
> Golden, CO 80401
> 303-384-6345 office
> 303-887-0149 cell
>
>
>
>
>
> On 4/3/12 2:39 PM, "Albert" <mailmd2011.gmail.com> wrote:
>
>> Hi Mike:
>> thanks a lot for kind advices.
>> yes, there are also several .top file.
>>
>> best
>>
>>
>>
>> On 04/03/2012 10:35 PM, Crowley, Michael wrote:
>>> Albert,
>>> Try doing the merge, merging each section (bonds, angles, ...) of each
>>> file into one file.
>>> Once that is done, try running charmm with the new parameter file
>>> instead
>>> of multiple files, making sure the energies match (even better check the
>>> forces using coor force/write coor). If the match is good, then you can
>>> write out a new psf for the new parameter file to use in chamber.
>>> Are there multiple topology files also (I noticed *.top in your
>>> command)?
>>> Mike
>>>
>>
>>
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Received on Tue Apr 03 2012 - 15:30:03 PDT
