Re: small query...

From: Gaurav Sharma (sharma_at_coe.neu.edu)
Date: Fri Nov 17 2006 - 21:15:50 CST

Harish,

Here is the correct sequence of commands:

segment B {
pdb chainB.pdb
residue 30 THR
}
coordpdb chainB.pdb B

Gaurav

hl332_at_drexel.edu wrote:

>Hi Gaurav,
> Thanks for your reply but it didnt work.Please see below what i was trying to do:
>
>Residue missing: 30 (resid)
>From: Chain B (segname B)
>resname: THR
>other than all things in pgn script, i used as you suggested:
>
>segment B {pdb chainB.pdb}
>{
> residue 30 THR
> coordpdb chainB.pdb B
>}
>also i tried this: it didnt work either
>
>segment B {pdb chainB.pdb}
>{
> residue 30 THR
> coordpdb chainB.pdb B
>}
>
>It is showing INVALID COMMAND NAME in both cases. Can you tell me what is going wrong?? Have you done yourself something of this kind in using vmd?
>
>regards n thanks
>Harish
>-------------------------------------------------
>Harish Vashisth (Ph.D Candidate)
>CAT-361,Chemical & Biological Engg.
>Drexel University, Philadelphia, PA
>office: 215-895-5823
>
>----- Original Message -----
>From: Gaurav Sharma <sharma_at_coe.neu.edu>
>Date: Wednesday, November 15, 2006 8:56 pm
>Subject: Re: namd-l: small query...
>
>
>
>>Harish,
>>
>>In the segment section of your pgn file just add the following line:
>>residue xxx YYY
>>
>>Where xxx is the position (resid) where you want to add the YYY
>>residue.
>>Gaurav
>>
>>
>>
>>
>>hl332_at_drexel.edu wrote:
>>
>>
>>
>>>Hi,
>>> This might sound like a simple and dumb question but "How can i
>>>
>>>
>>put whole missing residue into my new pdb while using psfgen".
>>Second thing, what if this residue is missing from end rather than
>>middle of my protein (insulin)? I have actually just one file of
>>the kind i want in whole P.data bank and it seems i need to repair
>>it. It might take a minute for more experienced people out there to
>>clarify.>
>>
>>
>>>Thanks in Advance..
>>>
>>>Harish
>>>
>>>
>>>
>>>
>>--
>>Gaurav Sharma
>>Computational BioNano Robotics Lab
>>Northeastern University
>>Boston, MA - 02115
>>Tel: 617-373-2970
>>http://www.bionano.neu.edu/
>>
>>
>>
>>
>>

-- 
Gaurav Sharma
Computational BioNano Robotics Lab
Northeastern University
Boston, MA - 02115
Tel: 617-373-2970
http://www.bionano.neu.edu/ 

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