Re: Issue with preparing QM-MM

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Feb 27 2020 - 16:02:54 CST

I Victor
setting up QM-MM needs a psf and a related pdb

On Thu, Feb 27, 2020 at 9:45 PM Victor Kwan <vkwan8_at_uwo.ca> wrote:

> Hi Francesco,
>
> DCD files does not contain topological information (resid, etc), only the
> atom number. It does not matter if you load a psf containing resid 0 or
> resid 999 after you load the dcd.
>
> See: https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dcdplugin.html
>
> Kind regards,
>
> Victor Kwan
>
> Victor
>
> On Thu, Feb 27, 2020 at 3:28 PM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> 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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