Is the order in the file more important than running at optimal speed?
Solute atoms go before solvent atoms for the convenience of the solvent
optimizations. I suggest you just reorder PDB's before using them for
whatever is so vital.
Bill
On 10/10/19 7:09 AM, Dawid das wrote:
> Dear Amber Users,
>
> I struggle with one more problem. Namely in my PDB file, the order
> of units is the following:
>
> protein
> water
> ions (Na+, Cl-)
>
> But saveAmberParam yields *parm and *rtp files with the following order
>
> protein
> ions (Na+, Cl-)
> water
>
> I tried to change the order of loading libraries for ions and solvents but
> it doesn't work. It's really important for me to conserve the order from
> PDB file. How could I do it?
>
> Best regards,
> Dawid Grabarek
>
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Received on Thu Oct 10 2019 - 07:30:02 PDT
