Hi,
Now I realized that inpcrd files are different.
For the energy calculation, I used 1.rst (from glycam-web) with 1.parm7
of glycam-web. For the amber output files, I used prmtop and inpcrd
files as saveAmberparm yielded. I see that those coordinate files are a
bit difference.
If I use 1.rst with Amber-generated prmtop file, I obtain nearly
identical energies as
Konsole output
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.9868E+02 4.1747E+00 1.5639E+01 O5 5
BOND = 3.4740 ANGLE = 7.0702 DIHED =
-7.2685
VDWAALS = -14.1628 EEL = -302.0293 HBOND =
0.0000
1-4 VDW = 21.4657 1-4 EEL = 590.1347 RESTRAINT = 0.0000
for Amber prmtop and
Konsole output
Konsole output
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.9868E+02 4.1747E+00 1.5639E+01 O5 5
BOND = 3.4740 ANGLE = 7.0701 DIHED =
-7.2684
VDWAALS = -14.1628 EEL = -302.0293 HBOND =
0.0000
1-4 VDW = 21.4657 1-4 EEL = 590.1347 RESTRAINT = 0.0000
for glycam 1.parm7.
I also attach coordinate files, if they are relevant.
When creating prmtop and inpcrd files from amber, I used the same leaprc
file (also attached).
Batuhan
On 09/21/15 15:55, Lachele Foley wrote:
> Are you certain that you are using exactly the same parameter files to
> create each?
>
>
> On Mon, Sep 21, 2015 at 9:35 AM, Jason Swails <jason.swails.gmail.com> wrote:
>> On Mon, Sep 21, 2015 at 8:45 AM, Batuhan Kav <bkav13.ku.edu.tr> wrote:
>>
>>> 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?
>>>
>> No. They are definitely not the same. You can see where the differences
>> are by comparing the energy components.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Sep 21 2015 - 07:30:04 PDT
