Re: fixed residue

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Mon Jul 28 2008 - 23:38:10 CDT

p.s. and you have to save whole file, not just the line you changed!!!

On Tue, Jul 29, 2008 at 12:36 AM, Roman Petrenko <rpetrenko_at_gmail.com> wrote:
> suppose you want to fix CA atom of residue number 2. in your input
> file myfile.pdb file you have a line
>
> ATOM 25 CA GLY A 2 -0.164 2.464 -3.421 1.00 0.00 C
>
> change it to
> ATOM 25 CA GLY A 2 -0.164 2.464 -3.421 1.00 1.00 C
>
> and save as myfile_fixed.pdb
>
> then add the following three lines to namd config file (anywhere
> before "run" statement)
>
> fixedAtoms on
> fixedAtomsFile myfile_fixed.pdb
> fixedAtomsCol B
>
>
>
> On Mon, Jul 28, 2008 at 11:49 PM, Rudra Banerjee <bnrj.rudra_at_yahoo.com> wrote:
>> As a beginner with NAMD, i am puzzelesd over how i can fix the atom position!
>> i
>> have Glu residue solvated in water. Now i want glutamines to be fixed.
>> so if i use fixedAtoms tag on, what should i put in the
>> fixedAtomfiles? the PDB file name of the gultamine?
>> plz help
>>
>>
>> --
>> Rudra
>> JRF; SNBNCBS
>> http://www.bose.res.in/~rudra
>>
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>>
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>> Why?See: http://www.gnu.org/philosophy/no-word-attachments.html
>>
>>
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>>
>
>
>
> --
> Roman Petrenko.
> Physics Department
> University of Cincinnati
>

-- 
Roman Petrenko.
Physics Department
University of Cincinnati

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