[gmx-users] DNA with charmm27 works fine but why

[Justin Lemkul]

On 2/4/14, 12:52 PM, gromacs query wrote:
>>> When running grompp, yes, the order is significant and the coordinates
> must match the topology.
>
> am little confused about 'coordinates'. Say if I have two structures which
> are well equlibrated and just represent two different configurations and
> also the atom order matches with some common top file then even I can not
> use same .top file?
>

The coordinate values don't matter.  The contents of the coordinate file 
matters, i.e. the order of the atoms present in the coordinate file must match 
the order of the topology.  If that is not the case, grompp complains very loudly.

-Justin

>
> On Tue, Feb 4, 2014 at 5:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/4/14, 12:35 PM, gromacs query wrote:
>>
>>> Hi Justin
>>>
>>>   Presence of the correct atoms is the only absolute requirement
>>>>>
>>>>
>>> Thanks. Correct 'atoms' mean correct 'atom names'? so does that mean I
>>> should rename my atoms according to rtp file?
>>>
>>>
>> Yes, atom names need to match.  That's all that's in a coordinate file,
>> anyway.
>>
>>
>>   Also one more question: I think atom order does matter when I load a pdb
>>> and use some .top file? (and if I understood it correctly; if I am using
>>> from rtp file, which is a sort of residue library file, then order does
>>> NOT
>>> matter)
>>>
>>>
>> When running grompp, yes, the order is significant and the coordinates
>> must match the topology.  That is because bonded geometry, exclusions, etc.
>> are based on atom numbers, which follow a specific order.  pdb2gmx is a bit
>> smarter (surprisingly) in terms of sorting out the atoms it finds, but at
>> the point that it loads the .rtp and checks the input coordinate file, all
>> it is doing is making sure all the atoms it needs are present.  Bonds and
>> things are assigned later.
>>
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> 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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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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