Le 22/09/2010 09:52, Trevor Gokey a écrit :
> Hi,
>
> I can't seem to find the tutorial you're referencing (or I can't find the proper vmd section) so I'm not sure how the tutorial told you to load the inpcrd... but inpcrds will appear correctly if you display them is as amber restart files. Does using this setting help any?
>
> Trevor
Thanks Trevor, I have used the "AMBER coordinates" instead of the
"AMBER restart" setting when I have loaded my inpcrds.
> On Tue, Sep 21, 2010, Baptiste Legrand wrote:
>
>> So, the positive total energy (~ 5.0 10+1) observe after the
>> minimization could be related to the wrong parametrization of the gaff
>> forcefield for this type of molecule? (with non classical peptidic bond
>> but CO-NH-NH-C (side chain)-CO-NH-NH-...). Thanks
> Why do you think a positive energy is "bad"? The zero of energy is arbitrary.
> You should see if minimization moves the structure away from a "good" starting
> point by too large an amount.
>
> ....dac
>
>
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Well, I thought that a positive energy was unfavorable and means that my
initial structure was really "bad" (bad angles, steric clashs etc...).
These are the first and the last step of the minimization, it doesn't
seem to be bad. The energy decrease from 2.3221E+02 to 3.9699E+01. I
will read the chapter about the energies in the amber manual.
NSTEP ENERGY RMS GMAX NAME NUMBER
1 2.3221E+02 3.1148E+01 1.5869E+02 C2 56
BOND = 54.0796 ANGLE = 82.7820 DIHED =
78.4045
VDWAALS = -4.4471 EEL = -96.1161 HBOND =
0.0000
1-4 VDW = 24.8639 1-4 EEL = 92.6435 RESTRAINT =
0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
52000 3.9699E+01 3.2797E-04 1.3263E-03 C5 38
BOND = 2.8199 ANGLE = 11.0717 DIHED =
30.4281
VDWAALS = -12.5402 EEL = -113.4219 HBOND =
0.0000
1-4 VDW = 20.0602 1-4 EEL = 101.2809 RESTRAINT =
0.0000
Best regards,
Baptiste
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Received on Wed Sep 22 2010 - 08:00:10 PDT
