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

Justin Lemkul jalemkul at vt.edu
Tue Feb 4 18:40:53 CET 2014

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 



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


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