Thanks for reply I will do as you have suggested.
I have one more query
I have earlier posted mail regarding it.
I have to do water mediated H-Bond analysis to do this I have processed mdcrd file
using ptraj command:
closest 10 :115
Also generate new prmtop contain protein-DNA complex and 10 water.
When I visualized the processed mdcrd file some long bonds are there, selected
10 water molecules were also there in processd mdcrd file.
I have a question when I am generating new prmtop taking any of the 10 molecule in
modified PDB to generate prmtop.
How ptraj processing the mdcrd file so that it contain 10 water molecules.
So here numbring will not affect the overall process as well as visualiztion?
> Since you have the same version of ptraj with the same bugfixes
> applied on both systems, yet the one on your cluster works and the one
> you have locally does not, this leads me to believe that maybe the
> patches did not get applied correctly to the one you have locally. If
> possible, try to start with a fresh copy of AT1.4 on your local
> system, then apply the bugfixes, then compile and see if the error
> still occurs.
>
> -Dan
>
> On Thu, Mar 3, 2011 at 11:25 AM, Sangita Kachhap <sangita.imtech.res.in> wrote:
>> Yes both have same version.
>>
>>> Is the version of ptraj on your cluster that works from AT 1.4 with
>>> all bugfixes applied?
>>>
>>> -Dan
>>>
>>> On Thu, Mar 3, 2011 at 10:59 AM, Sangita Kachhap <sangita.imtech.res.in>
>>> wrote:
>>>> Thanks Daniel
>>>> You are right this may be bug error when I ran taht mdcrd file in cluster it
>>>> was
>>>> fine
>>>> but when again ran in my local system gave the same warning.
>>>>
>>>> But in my local system I already have applied all bugfix from
>>>> http://ambermd.org/bugfixesat.html
>>>>
>>>> Whey then this error is?
>>>>
>>>>
>>>>> Hi,
>>>>>
>>>>> First, have you applied all bugfixes to AT 1.4?
>>>>>
>>>>> http://ambermd.org/bugfixesat.html
>>>>>
>>>>> Second, is there some reason to suspect that your trajectory is
>>>>> corrupted (as is indicated by the warning message)? If not, check to
>>>>> make sure your topology matches your trajectory (which can also cause
>>>>> that message).
>>>>>
>>>>> -Dan
>>>>>
>>>>> On Thu, Mar 3, 2011 at 7:33 AM, Sangita Kachhap <sangita.imtech.res.in>
>>>>> wrote:
>>>>>> Hello all
>>>>>> I am doing distance measurement betwen two atoms.
>>>>>> I have done it for a mdcrd file of 2ns run when I am doing for another
>>>>>> which
>>>>>> is
>>>>>> in continuation
>>>>>> mdcrd file I am getting the following error:
>>>>>>
>>>>>> checkCoordinates(): Could not predict number of frames for AMBER
>>>>>> trajectory
>>>>>> file: combined_md_prod7.mdcrd
>>>>>> If this is not a compressed file then there is a problem
>>>>>>
>>>>>> WARNING in transformDistance(): Blowing array; too many frames!!
>>>>>>
>>>>>>
>>>>>> WARNING in transformDistance(): Blowing array; too many frames!!
>>>>>>
>>>>>>
>>>>>> WARNING in transformDistance(): Blowing array; too many frames!!
>>>>>>
>>>>>>
>>>>>> WARNING in transformDistance(): Blowing array; too many frames!!
>>>>>>
>>>>>>
>>>>>> ERROR in safe_malloc: Error in alloc of -8 bytes
>>>>>>
>>>>>> Can anybody please suggest where is the problem.
>>>>>>
>>>>>>
>>>>>> With regard
>>>>>> Sangita Kachhap
>>>>>> JRF
>>>>>> BIC,IMTECH
>>>>>> CHANDIGARH
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
>>>>
>>>> Sangita Kachhap
>>>> JRF
>>>> BIC,IMTECH
>>>> CHANDIGARH
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
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Received on Thu Mar 03 2011 - 09:30:03 PST
