[gmx-users] Regarding genconf

[nikhil damle]

Hi Vinod,

How did you build your top file for input to grompp ? genconf would have given you a multiplied system in .gro structure format. I think you should generate .top file from this .gro file using pdb2gmx and then use that as grompp  input.


Regards,
Nikhil


________________________________
From: jani vinod <genomejani at gmail.com>
To: gmx-users at gromacs.org
Sent: Fri, 4 June, 2010 10:54:16 AM
Subject: [gmx-users] Regarding genconf

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.


Thanks
vinod 


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