Dear Jason,
Thank you for the answer. I checked the energies for both file sets and
obtained 2.9871E+02 from one and 2.9268E+02 from the other. So, they are
not identical, but since they are very close to each other, d o you
think it will be safe to assume both files are the same?
Batuhan Konsole output
Konsole output2.9871E+02 Konsole output 2.9871E+02
On 09/21/15 13:18, Jason Swails wrote:
> On Mon, Sep 21, 2015 at 6:23 AM, Batuhan Kav <bkav13.ku.edu.tr> wrote:
>
>> Dear All,
>>
>> I am trying to set up a simple carbohydrate simulation in Amber. I
>> observe some differences between leap and glycam-web generated parameter
>> files. I would like to ask what might be the reason for such difference.
>>
>> So, here are the details. I created a pdb file in glycam-web builder.
>> Then, glycam-web gives me 1_Amber.pdb, which I think is ready to be used
>> in leap. Glycam-web also gives me 1.parm7 file.
>>
>> I delete connectivity from 1_Amber.pdb, and load it into leap using
>> Glycam-06 parameters. Then, I create the amber parameter files using
>> saveAmberparm.
>>
>> When I compare two parameter files, I observe some differences. For
>> instance, in some flags like BOND_FORCE_CONSTANT and ANGLE_EQUIL_VALUE,
>> the number of entries are different for each file. So I wonder what
>> might I be doing wrong here? I was expecting to obtain nearly identical
>> files with the both procedures.
>>
> Two prmtops can give identical energies and forces but still be very
> different if you simply compare their contents. The best way to really
> compare two prmtops is to calculate the energy with the same set of
> coordinates for both topology files and make sure it comes out identical.
>
> HTH,
> Jason
>
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Received on Mon Sep 21 2015 - 06:00:10 PDT
