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From: Gregorio Alanislobato (gregorio.alanislobato_at_kaust.edu.sa)
Date: Tue Aug 17 2010 - 18:26:08 CDT
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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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