AMBER Archive (2008)

Subject: Re: AMBER: rms

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed May 14 2008 - 09:01:17 CDT

Hi Urszula,

Does the COM.x file contain the residues you want to fit ? It should at
least have residues 1 to 126 if its a pdb file. If its not a pdb file it
should have all atoms that are present in the topology file.
If you still didnt solve this problem, you could send me the ptraj
logfile to see what's wrong.

Best
vlad

Urszula Uciechowska wrote:
> this is the script that i am using:
>
>
> trajin ../PROD1.mdcrd
> trajin ../PROD2.mdcrd
> trajin ../PROD3.mdcrd
> trajin ../PROD4.mdcrd
> trajin ../PROD5.mdcrd
> trajin ../PROD6.mdcrd
> trajin ../PROD7.mdcrd
> trajin ../PROD8.mdcrd
> reference ../COM.x
> rms reference :1-275 out rmsd.rec.out time 0.4
> rms reference :276 out rmsd.lig.out time 0.4
> rms reference :1-276 out rmsd.com.out time 0.4
>
> Is it something wrong with it?
>
> Best Regards,
> Urszula Uciechowska
>
> MSc.PhD Student
> Medicinal Chemistry Group
> University of Halle-Wittenberg
>
> ----- Original Message -----
> From: Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
> Date: Monday, May 12, 2008 2:45 pm
> Subject: Re: AMBER: rms
> To: amber_at_scripps.edu
>
>
>
>> Hi Urszula
>>
>> Could you tell us the script you are using to do that? My impression
>> is
>> that your mask is not correct.
>>
>> Best
>> vlad
>>
>> Urszula Uciechowska wrote:
>>
>>> Dear Amber users,
>>>
>>> I am trying to calculate rms with ptraj, but after loading my
>>>
>> trajectory files i keep
>>
>>> having
>>>
>>> ERROR in rms: KRMS_ reported Number of atoms less than 2
>>>
>>> and the program quits. What is wrong?
>>> thanks a lot for any help
>>>
>>> Best Regards,
>>> Urszula Uciechowska
>>>
>>> MSc.PhD Student
>>> Medicinal Chemistry Group
>>> University of Halle-Wittenberg
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>> --
>> ----------------------------------------------------------------------------
>> Dr. Vlad Cojocaru
>>
>> EML Research gGmbH
>> Schloss-Wolfsbrunnenweg 33
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533266
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>> EML Research gGmbH
>> Amtgericht Mannheim / HRB 337446
>> Managing Partner: Dr. h.c. Klaus Tschira
>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>> http://www.eml-r.org
>> ----------------------------------------------------------------------------
>>
>>
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> 

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
http://www.eml-r.org
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