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

[gromacs query]

>> 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?


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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