[gmx-users] Regarding genconf

[Justin A. Lemkul]

jani vinod wrote:
> Hello,
> I build a system solvated in water .
> Then replicated the system using genconf. Now when I am running grompp i am
> getting following warning
> Warning: atom name 404 in PH7.top and replicate_systemB.gro does not 
> match (N - C1)
> Warning: atom name 405 in PH7.top and replicate_systemB.gro does not 
> match (H1 - C2)
> Warning: atom name 406 in PH7.top and replicate_systemB.gro does not 
> match (H2 - C3)
> Warning: atom name 407 in PH7.top and replicate_systemB.gro does not 
> match (H3 - N4)
> Warning: atom name 408 in PH7.top and replicate_systemB.gro does not 
> match (CA - C5)
> Warning: atom name 409 in PH7.top and replicate_systemB.gro does not 
> match (CB - C6)
> Warning: atom name 410 in PH7.top and replicate_systemB.gro does not 
> match (CG - O7)
> Warning: atom name 411 in PH7.top and replicate_systemB.gro does not 
> match (OD1 - P8)
> Warning: atom name 412 in PH7.top and replicate_systemB.gro does not 
> match (OD2 - O9)
> Warning: atom name 413 in PH7.top and replicate_systemB.gro does not 
> match (C - O10)
> Warning: atom name 414 in PH7.top and replicate_systemB.gro does not 
> match (O - O11)
> Warning: atom name 415 in PH7.top and replicate_systemB.gro does not 
> match (N - C12)
> Warning: atom name 416 in PH7.top and replicate_systemB.gro does not 
> match (H - C13)
> Warning: atom name 417 in PH7.top and replicate_systemB.gro does not 
> match (CA - O14)
> Warning: atom name 418 in PH7.top and replicate_systemB.gro does not 
> match (CB - C15)
> Warning: atom name 419 in PH7.top and replicate_systemB.gro does not 
> match (C - O16)
> Warning: atom name 420 in PH7.top and replicate_systemB.gro does not 
> match (O - C17)
> Warning: atom name 421 in PH7.top and replicate_systemB.gro does not 
> match (N - C18)
> Warning: atom name 422 in PH7.top and replicate_systemB.gro does not 
> match (H - C19)
> Warning: atom name 423 in PH7.top and replicate_systemB.gro does not 
> match (CA - C20)
> 
> and when after ignoring the warning I try to run system my system get 
> distorted.
> 

Whenever grompp throws warnings like this, don't ignore them and plow ahead, 
it's a recipe for disaster.  The [molecules] section of your topology is out of 
order with respect to your coordinate file, so parameters for different species 
are being applied incorrectly.

-Justin

> 
> Thanks
> vinod
> 

-- 
========================================

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

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