Re: [AMBER] error with chamber

From: Crowley, Michael <Michael.Crowley.nrel.gov>
Date: Tue, 3 Apr 2012 14:35:36 -0600

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

-- 
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 2:28 PM, "Albert" <mailmd2011.gmail.com> wrote:
>Hi Mike:
>   thank you very much for your kind messages.
>   Yes, it requires prm for protein, lipids and ligand.... and they are
>in separate files.....
>
>best
>Albert
>
>
>On 04/03/2012 10:25 PM, Crowley, Michael wrote:
>> Albert,
>> Ah, you have multiple param files and you need them all?
>> Are they used in charmm as:
>>   read param card name file1.prm
>>   read param card append name file2.prm
>> ???
>>
>> If so, then you have some work cut out for you.
>> We have not implemented the flexibility of multiple topology and
>>multiple
>> parameter files. You will have to merge them by hand.
>> Be very very careful about atom types. If you need more info on merging,
>> let me know.
>> Mike
>>
>
>
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Received on Tue Apr 03 2012 - 14:00:03 PDT