[gmx-users] Mass and charge data are missing in [ atomtypes ] section.

[Dd H]

Thank you so much!

On 13 October 2016 at 20:07, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/12/16 11:06 PM, Dd H wrote:
>
>> I found these words in the GROMACS v4.5.5 manual:
>>
>> *[ atoms ] : defines the molecule, where nr and type are fixed, the rest
>> is
>> user defined. So*
>> *atom can be named as you like, cgnr made larger or smaller (if possible,
>> the total charge of a **charge group should be zero), and charges can be
>> changed here too.*
>>
>> So does it means the mass and charge of [ atomtypes ] section could be
>> modified in [ atoms ] section?
>>
>>
> Look at the example in section 5.7.2.  Note that masses are absent.  If
> masses are not provided in [atoms], they are referenced from [atomtypes].
> Charges present in [atomtypes] are never used for anything and must be
> specified in [atoms].
>
> -Justin
>
>
> On 12 October 2016 at 23:30, Alan <alanwilter at gmail.com> wrote:
>>
>> But read the GMX manual to understand why it's all fine.
>>>
>>> On 12 October 2016 at 13:29, Dd H <ddhecnu at gmail.com> wrote:
>>>
>>> Thank you!
>>>>
>>>> On 12 October 2016 at 19:50, Alan <alanwilter at gmail.com> wrote:
>>>>
>>>> It's all fine.
>>>>>
>>>>> On 12 October 2016 at 12:34, Dd H <ddhecnu at gmail.com> wrote:
>>>>>
>>>>> I use this command:
>>>>>> acpype -p filename.prmtop -x filename.inpcrd
>>>>>>
>>>>>> It generates parameter files for GROMACS and my question is about the
>>>>>>
>>>>> .top
>>>>>
>>>>>> file of outputs.
>>>>>>
>>>>>> On 12 October 2016 at 18:22, Alan <alanwilter at gmail.com> wrote:
>>>>>>
>>>>>> Which acpype command did you specifically used?
>>>>>>>
>>>>>>> acpype may be able to use Antechamber and calculate partial
>>>>>>>
>>>>>> charges.
>>>
>>>> See
>>>>>
>>>>>> acpype -h
>>>>>>>
>>>>>>> On 12 October 2016 at 09:56, Dd H <ddhecnu at gmail.com> wrote:
>>>>>>>
>>>>>>> Hi everyone,
>>>>>>>> I generated a .top file of a ligand using acpype for MD
>>>>>>>>
>>>>>>> simulations.
>>>>
>>>>> There
>>>>>>>
>>>>>>>> are some new atom types in [ atomtypes ] section, but the data of
>>>>>>>>
>>>>>>> mass
>>>>>
>>>>>> and
>>>>>>>
>>>>>>>> charge columns of the section are zeros. However they can be
>>>>>>>>
>>>>>>> found
>>>
>>>> in
>>>>
>>>>> the [
>>>>>>>
>>>>>>>> atoms ] section. Can you tell me if this file is ok for MD
>>>>>>>>
>>>>>>> simulations?
>>>>>
>>>>>> Thank you in advance!
>>>>>>>>
>>>>>>>> Dading Huang
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>>>>>>> --
>>>>>>> Alan Wilter SOUSA da SILVA, DSc
>>>>>>> Senior Bioinformatician, UniProt
>>>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>>>> European Molecular Biology Laboratory
>>>>>>> Wellcome Trust Genome Campus
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>>>>>
>>>>> --
>>>>> Alan Wilter SOUSA da SILVA, DSc
>>>>> Senior Bioinformatician, UniProt
>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>> European Molecular Biology Laboratory
>>>>> Wellcome Trust Genome Campus
>>>>> Hinxton
>>>>> Cambridge CB10 1SD
>>>>> United Kingdom
>>>>> Tel: +44 (0)1223 494588
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>>>
>>> --
>>> Alan Wilter SOUSA da SILVA, DSc
>>> Senior Bioinformatician, UniProt
>>> European Bioinformatics Institute (EMBL-EBI)
>>> European Molecular Biology Laboratory
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridge CB10 1SD
>>> United Kingdom
>>> Tel: +44 (0)1223 494588
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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