VMD-L Mailing List

From: Gregorio Alanislobato (gregorio.alanislobato_at_kaust.edu.sa)
Date: Tue Aug 17 2010 - 19:51:10 CDT

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
>>
>>
>
>
>
>