VMD-L Mailing List

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

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
>
>