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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
