the "step4.1_equilibration" output here doesn't match what you sent before.
this one goes to a density of 1 rather quickly, which Prof Case mentioned
was a problem in the previous one. Maybe you need to send updated
information about the problem observed with these specific outputs - I
didn't see any error in the files that you attached.
On Tue, Feb 7, 2023 at 10:37 AM Prithviraj Nandigrami <
prithviraj.nandigrami.gmail.com> wrote:
> Thank you, Dr. Case and Dr. Simmerling for your helpful suggestions. The
> input pdb file was processed through 'pdb4amber' prior to system
> preparation using tleap.
>
> Here are the commands I used to prepare and solvate the system in tleap:
>
> parm10 = loadamberparams parm10.dat
> loadOff terminal_monophosphate.lib
> source leaprc.water.tip3p
> loadAmberParams frcmod.tip3p
> loadamberparams M6A.frcmod
> M6A = loadMol2 M6A.mol2
> addions mol Na+ 0
> solvateOct mol TIP3PBOX 12.0 0.75
> saveAmberParm mol 2L1F.GAACA.M6A.parm7 2L1F.GAACA.M6A.rst7
>
> I also attached the pdb4amber output file (before tleap) and the output
> prepared system after tleap, as well as the output log file for tleap.
> Also, attached is the AMBER minimization and equilibration log files.
>
> I would appreciate any help regarding this.
>
> Sincerely,
> PN
>
>
>
>
>
>
> On Tue, Feb 7, 2023 at 8:26 AM David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Mon, Feb 06, 2023, Prithviraj Nandigrami via AMBER wrote:
>> >This is what the density looks like in the mdout files:
>> >
>> >*Equilibration *
>> >
>> > 0.8121
>> > 0.7651
>> > 0.7322
>> > 0.7139
>> > 0.7063
>> ....
>> >*Production*
>> >
>> > 0.7694
>> > 0.7699
>> > 0.7722
>> > 0.7744
>> > 0.7767
>>
>> ...
>>
>> These are *very* low densities, certainly for a simulation of a
>> macromolecule in water. The fact that they don't quickly approach a value
>> near 1.0 (since most of a typical system is water) suggests some problem
>> with the setup of the system. I don't have enough info now to grok
>> what the most likely problem is there.
>>
>> ....dac
>>
>>
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Received on Wed Feb 08 2023 - 04:30:02 PST
