From: Alex Balaeff (abalaeff_at_polarisqb.com)
Date: Mon Aug 31 2020 - 00:41:26 CDT
Zhihong:
What error did you get? Please include the log file with the error
description and your namd script.
Just looking at the file you've sent, I have the following comments:
1) Your beta column is set to 1 which indicates to NAMD that you want to
restrain those atoms to their indicated positions with the force constant
of 1 kcal/(mol*A^2). I suggest setting the constant to 5 or 10
kcal/(mol*A^2)
2) Don't restrain hydrogens. Restraining the heavy atoms is quite enough.
Unless the Hs in your simulation move wildly and you do need to restain
them as well.
3) Do use separate PDB files to flag the restrained atoms and QM atoms. In
the QM file, you need both beta and occupancy columns, since your QM
subsystem seems to be covalently bound to the MM subsystem.
4) Your QM system selection seems to include water molecules ## 75, 76,
etc.; is that what you wanted? If not, edit your VMD selection:
set QM [atomselect top "(protein and resid 75 76 77 144 193 238 268) or
(resname DMP) or (resname TIP3 and resid 4231)"]
(please double-check whether this selection does include every residue you
wanted into the QM region and correct as needed)
Best,
Alexander.
On Sun, Aug 30, 2020 at 10:32 AM 辛志宏 <xzhfood_at_njau.edu.cn> wrote:
>
> Thank you Alexander,
> I restrain the QM atom as follows,but a new error occured regarding to QM
> atom assignment, how to fixed it ? I attached the my QM file here.
> constraints on
> consexp 2
> consref ./YZZ-QMMM_fixed.pdb
> conskfile ./YZZ-QMMM_fixed.pdb
> conskcol B
>
> Thank you again.
> Zhihong Xin
>
>
>
>
> From: Alex Balaeff <abalaeff_at_polarisqb.com>
> Date: 2020-08-29 22:29:48
> To: namd-l_at_ks.uiuc.edu,"辛志宏" <xzhfood_at_njau.edu.cn>
> Subject: Re: namd-l: QM atom cannot be fixed in space
>
> Zhihong:
>
> My suggestion is to harmonically restrain the QM atom rather than to keep
> it fixed. If you want to limit the movement of your QM molecule around the
> simulation cell, the effect is going to be the same. See
> https://www.ks.uiuc.edu/Research/namd/2.14/ug/node29.html , "Position
> restraint"
>
> Also I suggest to keep the QM region PDB and the restraint PDB as two
> separate files. Makes it easier to change things if needed (e.g., if you
> need to gradually lift the harmonic restraint).
>
> Best,
>
> Alexander.
>
>
>
>
>
>
>
>
>
>
> On Sat, Aug 29, 2020 at 8:53 AM 辛志宏 <xzhfood_at_njau.edu.cn> wrote:
>
>> Dear ALL,
>> An ERROR occured when I run QM/MM by NAMD, the error information and the
>> QM region setup as follows:
>>
>> 。。。。。。。。。。。。。。。。。。。
>>
>> ERROR: QM atom cannot be fixed in space!
>> FATAL ERROR: Error processing QM information.
>>
>>
>>
>> QM region setup:
>>
>> set allatoms [atomselect top all]
>> $allatoms set beta 0
>> $allatoms set occupancy 0
>> set QM [atomselect top "resid 75 76 77 144 193 238 268 299 4231"]
>> $QM set beta 1
>> $QM set occupancy 1
>> $allatoms writepdb YZZ-namd-QM.pdb
>>
>>
>>
>> Any suggestion will be much appreciate for fixing the issue, thank you
>> in advance.
>>
>>
>> Zhihong XIn
>>
>>
>>
>
> --
> -----
> Dr. Alexander Balaeff
> * Polaris Quantum Biotech www.PolarisQB.com <http://www.PolarisQB.com>*
> (919)-270-5772
>
>
>
-- ----- Dr. Alexander Balaeff * Polaris Quantum Biotech www.PolarisQB.com <http://www.PolarisQB.com>* (919)-270-5772
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:09 CST