[gmx-users] adding constraints

[Justin A. Lemkul]

subarna thakur wrote:
> Hi all,
> I want to add constraints for bond length of a ligand.Where do I place 
> the constraints statement in the .rtp file or in the .top file? 
>  

Are you looking to constrain only one single bond length?  If so, just add a 
[constraints] section to your topology.  The .rtp file won't do you any good, 
unless you're looking to build a complete .rtp entry and re-process with 
pdb2gmx, but I don't know if [constraints] is a valid entry in an .rtp file.

If you're looking to constrain all bond lengths, leave the topology alone and 
add "constraints = all-bonds" in your .mdp file.

-Justin

> Subarna Thakur
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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