AMBER Archive (2009)

Subject: Re: [AMBER] ouput trajectory of only CA atom

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Jul 08 2009 - 10:07:30 CDT

Dear Bala,

Yes you would need a topology file that contains only CAs. To my
knowledge, Leap cannot do that ... It would be nice feature though ...

What you can do is to create a pdb file with only the CAs and then use
that as topology file to visualize ... At least in VMD it works .. it
should in Pymol as well ...

 Vlad

Bala subramanian wrote:
> Hello,
>
> with just
>
> strip !@CA
>
> Ptraj works without any error. But when i make a pdb from the stripped
> trajectory, Ptraj shows the other atoms also in the pdb file. Do i need to
> create another prmtop consisting of only CA information to work with the
> trajectory of only CA atoms. I do not know if it is possible to create such
> a prmtop file for just the CA atoms. Is there any way to do the same ?
>
> Bala
>
> On Wed, Jul 8, 2009 at 4:41 PM, Carlos Simmerling <
> carlos.simmerling_at_gmail.com> wrote:
>
>
>> have you tried just
>> strip !@CA
>>
>> what exactly does ptraj say it is doing with your mask? it should tell you
>> #
>> atoms that match, etc.
>>
>> On Wed, Jul 8, 2009 at 9:24 AM, Bala subramanian
>> <bala.biophysics_at_gmail.com>wrote:
>>
>>
>>> Friends,
>>>
>>> How can i ask ptraj to output the coordinate of only the CA atoms from a
>>> trajectory file. I tried with following input but it vain. Is there
>>> anything
>>> wrong with the mask.
>>>
>>> trajin ub_anal.crd
>>> trajout ub_ca.crd
>>> strip @* &! @CA
>>>
>>>
>>> Thanks,
>>> Bala
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>>>
>>>
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-- 
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Dr. Vlad Cojocaru

EML Research gGmbH
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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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