Re: Issue with preparing QM-MM

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Feb 27 2020 - 14:28:19 CST

Hello Victor, of course, as implied in my "renumbering". 3 ,5 etc are
fictitious resid ID, which in reality were not in consecutive order. i am
trying to save the MD work that i did with resid 0.
Best
francesco

On Thu, Feb 27, 2020, 21:02 Victor Kwan <vkwan8_at_uwo.ca> wrote:

> Hello Francesco,
>
> ResID does not have to be in numerical order. I have attached a short
> proof of concept of 216 SWM4-NDP water that starts with resid 999. You can
> easily change the resid from 0 to 999 in your pdb and psf files.
>
> Kind regards,
>
> Victor
>
>
> On Thu, Feb 27, 2020 at 1:40 PM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> Hello
>>
>> My question is whether there is a way to circumvent the inability of
>> <prepare.qm.region.tcl> (vmd text mode) with nucleotides and a small
>> organic ligand, to recognize residue number 0 for the organic ligand
>>
>>
>> set seltext "(nucleic and resid 0 3 5 7 8 9)"
>>
>> the generated .QMonly.psf contains all except what relates to resid 0.
>> I understand that I could renumber the starting pdb and rebuild psf/pdb,
>> but I have already equilibrated the system with resid 0. Segname is not
>> useful here because it does not discriminate the nucleotides.
>>
>> Thanks for advice
>> francesco pietra
>>
>>
>>
>>

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