Hi Ross,
Thank you very much. This really strange since TYR residues are totally
unaffected by mutations. Anyway I think you are right regarding the
parameter files. Thank you very much for all your help.
Cristina
Ross Walker wrote:
> Hi Cristina,
>
> I took your input files and ran them in serial using sander v11 and the
> calculation crashes after 3 steps. Looking at the mdcrd file it is obvious
> there is a problem. Take a look at frame0 and frame2 attached. I zoomed in
> on the region where the problem occurs. Loading it into VMD it is obvious.
> This is what I meant when I said you should set ntwx=1 and then carefully
> look at each frame in VMD.
>
> It is clear you have some issue with the parameters here, or something else
> strange going on. It may be related to your mutations.
>
> I would start by investigating this.
>
> Good luck,
> Ross
>
>
>> -----Original Message-----
>> From: Cristina Sisu [mailto:csds2.cam.ac.uk]
>> Sent: Tuesday, June 22, 2010 9:10 AM
>> To: Ross Walker
>> Subject: Re: [AMBER] unexpected "vlimit exceeded for step" error
>>
>> Hi Ross,
>>
>> If I use a dt=0.001 and an ntlim=100 steps everything is fine for the
>> first simulation. If I take the rst file and use it as starting point
>> for the next simulation, the problem appears on step 60,
>> time(ps)=0.160.
>> If I have a larger ntlim = 500 steps, the problem appears at step 120.
>> If I use a different dt=0.002 then I start getting problems at step 3,
>> time(ps) = 0.006. I attach here the parameter and coordinate files as
>> well as the mdin files.
>> The mutations occured at residue 73.
>> This problem appeared recently with a set of 7 mutants, even though the
>> very same mutants in complex with an acylated ligand work absolutely
>> perfect (mutated a month ago). I wonder if something corrupted in
>> anyway the tleap version on my cluster and the prmtop/inpcrd files are
>> not reliable any more?
>>
>> Thank you for all your help,
>> Cristina
>>
>>
>> Ross Walker wrote:
>>
>>> Hi Cristina,
>>>
>>>
>>>
>>>> For the first 100 steps, everything runs smoothly, however when it
>>>> reaches 121st step, something happens and the systems stops
>>>>
>> recording
>>
>>>> the coordinates.
>>>>
>>>>
>>> This seems very strange. Can you try turning off the restraints and
>>>
>> see what
>>
>>> happens. Also did the location of where vlimit error occurred (step
>>>
>> number)
>>
>>> change when you switched to printing every step? If so then this
>>>
>> suggests
>>
>>> deeper problems. Have run the test cases and verified your AMBER
>>> installation is working correctly?
>>>
>>> If you can send me your prmtop, inpcrd and mdin files (by a direct
>>>
>> email,
>>
>>> not to the list) I will try running it here and see if I can
>>>
>> reproduce the
>>
>>> problem.
>>>
>>> All the best
>>> Ross
>>>
>>>
>>> /\
>>> \/
>>> |\oss Walker
>>>
>>> | Assistant Research Professor |
>>> | San Diego Supercomputer Center |
>>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>>>
>>> Note: Electronic Mail is not secure, has no guarantee of delivery,
>>>
>> may not
>>
>>> be read every day, and should not be used for urgent or sensitive
>>>
>> issues.
>>
>>>
>>>
>>>
>>> _______________________________________________
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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>
>
>
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Received on Thu Jun 24 2010 - 03:30:04 PDT
