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--- ----- Original Message ----- From: "Holger Gohlke" <gohlke.bioinformatik.uni-frankfurt.de> To: <amber.scripps.edu> Sent: Tuesday, April 12, 2005 2:30 AM Subject: Re: AMBER: MM_PBSA error > Xin Hu schrieb: >> >> Hi Holger, >> Thank you very much for your help. I looked over out sander program and >> there is only one parallel executable of "sander" (when I compiled the >> parallel version, it replaced the 'serial' version of sander). (Actually >> this version is both working for single and multiple processors.) >> >> As you suggested, should I go ahead to re-compile a "serial" amber >> again >> and get a "single-CPU sander" (named sander_serial)? so I can specify in >> the >> mm_pbsa.in file: SANDER /usr/local/amber8/exe/sander_serial". I will try >> to >> re-compile and let you know the result. > > Yes, this is what I would do. > > Best regards > > Holger > >> >> Thanks, >> >> Xin >> >> --- >> >> ----- Original Message ----- >> From: "Holger Gohlke" <gohlke.bioinformatik.uni-frankfurt.de> >> To: <amber.scripps.edu> >> Sent: Monday, April 11, 2005 4:49 PM >> Subject: Re: AMBER: MM_PBSA error >> >> > Hi, >> > >> > I think the problem is that the sander version that is called by >> > mm_pbsa >> > is the parallel version, which requires to set "mpirun" or the like in >> > front of the sander call. You should be able to circumvent this by >> > adding a line "SANDER <path_to_a_one_processor_version_of_sander>" to >> > the end of the mm_pbsa.in file (in the section .PROGRAMS). >> > >> > Best regards >> > >> > Holger >> > >> > >> > >> > Xin Hu schrieb: >> > >> > Dear Amber user >> > >> > I have a problem with the MM_PBSA calculation. I followed the examples >> > in /src/mm_pbsa/example/02_MMPBSA_Stability to run the calculation on >> > entropy energies, >> > >> > it showed an error: >> > >> > =>> Calculating energy / entropy contributions >> > Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.1 >> > Calc MM/GB/SAS >> > >> > Unit 6 Error on OPEN: sander_com.1.out >> > [0] MPI Abort by user Aborting program ! >> > [0] Aborting program! >> > p0_14716: p4_error: : 1 >> > /usr/local/amber8/exe/sander -O -i sander_com.in -o >> > sander_com.1.out -c ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.1 -p >> > ../ras_raf_II_wt.prmtop not successful >> > >> > I was aware that if I ingore the path specified in the command, or I >> > add >> > the full path (the working directory) to the output files, it works >> > properly. >> > >> > So I tried to modify the script in src/mm_pbsa, the script >> > "mm_pbsa_util.pm" or "mm_pbsa_calceneent.pm", attemping to delete the >> > path associated with command "sander", or adding >> > >> > path to the output file, however, neither way is working with errors >> > showing "compilation failed" "strict subs" etc. >> > >> > I wonder if anyone has caught the same problem and I appreciate for >> > help. The Amber8 is runnung on a linux cluster with MPI on parallel. >> > >> > Thanks, >> > >> > Xin >> > ----------------------------------------------------------------------- >> > The AMBER Mail Reflector >> > To post, send mail to amber.scripps.edu >> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu >> > >> >> ----------------------------------------------------------------------- >> The AMBER Mail Reflector >> To post, send mail to amber.scripps.edu >> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber.scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu >