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From: Gregorio Alanislobato (gregorio.alanislobato_at_kaust.edu.sa)
Date: Tue Aug 17 2010 - 19:51:10 CDT
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Hi,
Everything seemed to be working just fine with the parameter that Peter
recommended but now I get this error:
FATAL ERROR: disconnect replica 1
5.ready 0
I'll check if it has to do with the config files or the nodes I'm using.
Regards,
-- Gregorio Alanís Lobato, BSc 4700 KAUST Mail Box: 1899 Thuwal 23955–6900, KSA Student ID: 100037943 Badge #: 101969 Mobile Phone: +966-564-75-14-14 e-mail: gregorio.alanislobato_at_kaust.edu.sa On 17 August 2010 19:26, Gregorio Alanislobato < gregorio.alanislobato_at_kaust.edu.sa> wrote: > Thanks Peter, > > I'll check if that parameter helps... What force field do you recommend > instead of Shih's? > > Thanks in advance for your reply. > > > Regards, > -- > Gregorio Alanís Lobato, BSc > 4700 KAUST Mail Box: 1899 > Thuwal 23955–6900, KSA > Student ID: 100037943 > Badge #: 101969 > Mobile Phone: +966-564-75-14-14 > e-mail: gregorio.alanislobato_at_kaust.edu.sa > > > > On 17 August 2010 19:14, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote: > >> Hi Gregorio, >> >> Do you have >> paraTypeCharmm on >> in your config file? >> >> Regarding the use of the Shih et al. force field for folding proteins: >> don't do it. The force field in question wasn't designed for anything >> resembling that sort of simulation. >> >> Best, >> Peter >> >> On 08/17/2010 05:12 PM, Gregorio Alanislobato wrote: >> >> Hi, >> >> I'm performing a Replica Exchange MD but the protein I'm folding is a >> coarse grained model. I'm enqueuing my job with PBS and everything seems to >> work fine but I get the next error after a couple of seconds: >> >> SERVER: outputEnergies 1000 >> SERVER: dcdFreq 1000000 >> SERVER: source REcontrol.namd; run 0; save_array >> errpipe 4: ------------- Processor 0 Exiting: Called CmiAbort ------------ >> errpipe 4: Reason: FATAL ERROR: BAD BOND FORMAT IN XPLOR PARAMETER FILE >> errpipe 5: ------------- Processor 0 Exiting: Called CmiAbort ------------ >> errpipe 4: LINE=*BONDS* >> errpipe 5: Reason: FATAL ERROR: BAD BOND FORMAT IN XPLOR PARAMETER FILE >> >> I'm using the rbcg-2007.par file. It seems that NAMD's REMD tcl doesn't >> like the Bond format there... What can I do? >> >> Regards, >> -- >> Gregorio Alanís Lobato, BSc >> 4700 KAUST Mail Box: 1899 >> Thuwal 23955–6900, KSA >> Student ID: 100037943 >> Badge #: 101969 >> Mobile Phone: +966-564-75-14-14 >> e-mail: gregorio.alanislobato_at_kaust.edu.sa >> >> > > > >
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