Thanks! and please receive my apologies for not checking the help in the mdgx command… for some reason I thought the information of the mdgx -FITQ was the same that in the manual…
FixQ des exactly what I needed to do… and tether will also be handy for dealing with caps… I used NME and ACE caps for deriving the grids, and although I initially considered to fit the charges of the atoms in the caps, it is probably a better idea to keep these charges as those in the protein force field… (now I only have to decide from which force field I use the charges… you probably will recommend me ff15iq or ff14iq for consistency).
Best
Luis
> On 24 Feb 2021, at 14:25, David Cerutti <dscerutti.gmail.com> wrote:
>
> The keyword you need is FixQ (alias fixq). The input will look like this:
>
> &fitq
> (...)
> FixQ :1.CA 0.20
> FixQ :1.HA 0.10
> FixQ :1.N -0.30
> (...)
> &end
>
> Fixing the charges should also help to reduce the size of your matrix--if I
> programmed it right, and I think I did, the fixed charges will not get
> their own matrix columns but rather recede into the background. Another
> option you may want to consider comes in the form of the "Tether" and
> "TetherWeight" keywords. As implied, you can tether the resulting charges
> to the initial topology, so if you have charges that you like for any
> reason, you can supply those as an initial guess and the restraints will
> pull the charges towards those values as opposed to zero.
>
> When in doubt, always type "mdgx -FITQ" or "mdgx -YOUR_MODULE_NAME" on the
> command line. It will print a formatted reference for all* keywords in
> that module.
>
> Also note that the size of the matrix will not just be the numbers of atoms
> in all molecules--if you have many set to contain equal charges then this
> will drastically cut down on the matrix size. Make sure you are setting
> the maxmem / MaxMemory keyword to the actual amount of memory in your
> system--it's got a fairly low setting by modern standards owing to this
> module having come about back in 2011 or so. You can say "MaxMemory 16GB"
> and things like that--no need to type a big ugly number and worry about the
> number of zeros you included. Another thing to be aware of is the number
> of fitting points that you are taking per molecule. The matrix will come
> to (number of unique charges) x (number of data points in all molecules +
> number of charge value restraints + number of charge sum restraints). The
> numbers of restraints pale in comparison to the number of electrostatic
> potential fitting points, but you can set the density, selection, and total
> number of points with various keywords from the &fitq namelist. FitPoints
> is the upper limit per molecule conformation, but ProbeSig, ProbeEps,
> ProbeArm, and StericLimit are also pertinent to which points near the
> molecular surface are selected.
>
> Dave
>
> * All keywords that I remembered to add to the glossary feature. I'm sure
> I forgot one or two but there's always the reflector.
>
> On Wed, Feb 24, 2021 at 8:16 AM David Cerutti <dscerutti.gmail.com> wrote:
>
>> The keyword you need is FixQ (alias fixq). The input will look like this:
>>
>> &fitq
>> (...)
>> FixQ :1.CA 0.20
>> FixQ :1.HA 0.10
>> FixQ :1.N -0.30
>> (...)
>> &end
>>
>> Fixing the charges should also help to reduce the size of your matrix--if
>> I programmed it right, and I think I did, the fixed charges will not get
>> their own matrix columns but rather recede into the background. Another
>> option you may want to consider comes in the form of the "Tether" and
>> "TetherWeight" keywords. As implied, you can tether the resulting charges
>> to the initial topology, so if you have charges that you like for any
>> reason, you can supply those as an initial guess and the restraints will
>> pull the charges towards those values as opposed to zero.
>>
>> When in doubt, always type "mdgx -FITQ" or "mdgx -YOUR_MODULE_NAME" on the
>> command line. It will print a formatted reference for all* keywords in
>> that module.
>>
>> Dave
>>
>> * All keywords that I remembered to add to the glossary feature. I'm sure
>> I forgot one or two but there's always the reflector.
>>
>>
>>
>> On Wed, Feb 24, 2021 at 7:25 AM David A Case <david.case.rutgers.edu>
>> wrote:
>>
>>> ----- Forwarded message from Luis Simon <lsimon.usal.es> -----
>>>
>>> Date: Wed, 24 Feb 2021 09:34:30 +0100
>>> From: Luis Simon <lsimon.usal.es>
>>> To: amber.ambermd.org
>>> Subject: [AMBER] MDGX charge fitting with some charges fixed or restrained
>>>
>>> Dear Amber users:
>>>
>>>
>>> I wonder if there is any way of running mdgx charge fitting specifying a
>>> fixed charged for some of the atoms or group of atoms.
>>>
>>> “MinimizeQ" keyword request to fix all the charges restraining those of
>>> the group of atoms specified by the following atom mask to zero… is ti
>>> possible to restraint it to a different value than 0?
>>>
>>> I am trying to parametrize a set of molecules and I want to share the
>>> same charges with some of the atoms (just like amino acid backbone atoms
>>> share the same charges). MDGX allows this with the use of equalq keyword
>>> and the use of atom masks, but since the charges for all the molecules must
>>> be fitted simultaneously, my system run out of memory. A possibility would
>>> be to fit only a subset of the molecules (or even different subsets and use
>>> averages) and then transfer the charges of the backbone atoms to the rest
>>> of the molecules, for which the charges will be fitted separately. Is it
>>> possible to transfer them, fixing the charges of the common atoms?
>>>
>>> Thanks
>>>
>>> Luis
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>> ----- End forwarded message -----
>>>
>>
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Received on Wed Feb 24 2021 - 09:30:02 PST
