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

[Justin Lemkul]

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
>>>>>> Hinxton
>>>>>> Cambridge CB10 1SD
>>>>>> United Kingdom
>>>>>> Tel: +44 (0)1223 494588
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>>>>> --
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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
>>>> --
>>>> Gromacs Users mailing list
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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
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
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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

==================================================