VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Aug 18 2010 - 00:30:20 CDT

Hi Gregorio,
Well, that depends on what you want to learn... protein folding
simulations are still very much an unsolved problem, so at present
you're probably best off using one of the major all-atom force fields
(e.g., charmm22/cmap or AMBER ff03), and being extremely careful in your
force field choice, target system, and expectations.

Best,
Peter

On 08/17/2010 06:26 PM, Gregorio Alanislobato 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
> <mailto:gregorio.alanislobato_at_kaust.edu.sa>
>
>
>
> On 17 August 2010 19:14, Peter Freddolino <petefred_at_ks.uiuc.edu
> <mailto: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
>> <mailto:gregorio.alanislobato_at_kaust.edu.sa>
>
>
>
>
>