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 <genomej...@gmail.com> To: gmx-users@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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