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#206 - 11/14/08 09:24 AM Re: Sample scripts for basic tasks in CHARMM [Re: lennart]
ardie Offline
Forum Member

Registered: 03/28/08
Posts: 43
Thanks.

Quote:

If I had picked any other value you could still have asked the same question, so perhaps the number 30 is not so special.
You can change it to any other value that better suits your mood, or remove that part of the script if you want.



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#207 - 02/09/09 06:36 AM Re: Sample scripts for basic tasks in CHARMM [Re: lennart]
indrajit Offline
Forum Member

Registered: 12/11/08
Posts: 22
Loc: WestBengal, India
Respected Sir,
I have a problem using your stream file. I am trying to generate a truncated octahedron using the stream file set-up-truncated-octahedron.str file. But it is giving me the following output error message.

CHARMM> image byresidue select .not. SOLUTE end

***** LEVEL -2 WARNING FROM <CHARMM> *****
***** IMAGES NEED TO BE PRESENT
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5


I dont understand the error. What kind of error is it ? where and how do i get the image.

Please try to guide me. I will be highly thankful to you.

Indrajit Deb.
Research Scholar.
Dept. of Biophysics, molecular biology & bioinformatics.
Calcutta University.
India.

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#208 - 02/09/09 06:49 AM Re: Sample scripts for basic tasks in CHARMM [Re: indrajit]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
The stream file sets up the PBC with images. Did you modify it, or were there other errors prior to the one you report?
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#209 - 02/09/09 07:11 AM Re: Sample scripts for basic tasks in CHARMM [Re: lennart]
indrajit Offline
Forum Member

Registered: 12/11/08
Posts: 22
Loc: WestBengal, India
Respected Sir,
Thanks for reply, there are no prior error report.
Do charmm have to read any .img file like tips.img. I am waiting for your help.
Thanks


Edited by indrajit (02/09/09 07:12 AM)

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#210 - 02/09/09 11:59 AM Re: Sample scripts for basic tasks in CHARMM [Re: indrajit]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
It would help if you posted more of the output; as I said the script does normally setup PBC and images for you, so something unexpected must have happened before the error you posted. Does your system fulfill the stated assumptions for using the script, eg "PSF and coordinates from a system at least as large as the truncated octahedron have to be present"? One way to get this is to solvate your system in a sphere (solvate-sphere.str).
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#22579 - 10/21/09 05:26 PM Re: Sample scripts for basic tasks in CHARMM [Re: lennart]
Jun Offline
Forum Member

Registered: 10/19/09
Posts: 22
Hi,

I am a beginner using charmm.
I have a question about running script "gen-prot.inp". When reading sequence from PDB file, why do we use 4pti-a.pdb not 4pti.pdb ? Is it because of the number of peptide chain ?
Then, can we identify the number of peptide chain from the number of chain ID ?

Finally, how do you make 4pti-a.pdb from 4pti.pdb ?
Is there any script that change from 4pti.pdb to 4pti-a.pdb or do I need to change them by hand?

Thank you.

Jun

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#22581 - 10/22/09 02:12 AM Re: Sample scripts for basic tasks in CHARMM [Re: Jun]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
Yes it is because there is more than one chain in the original file; read the comments in the script.
Yes.
Editor.
There are probably lots scripts out there to do this. Note that you would already be finihsed with this task if you had simply done it instead of having to wait for an answer here.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#31052 - 12/02/12 03:27 PM Re: Sample scripts for basic tasks in CHARMM [Re: lennart]
Drishti Offline
Forum Member

Registered: 11/18/12
Posts: 33
Hey Lennart,

I am using your solvent-box script, the generated crd file contains 263 water molecules and the psf generated contains 252.

Is that normal or is their something weird that is going on somewhere?

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#31056 - 12/03/12 02:25 AM Re: Sample scripts for basic tasks in CHARMM [Re: lennart]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4688
Loc: ~ 59N, 15E
That should not happen.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#36659 - 11/17/17 01:09 AM Re: Sample scripts for basic tasks in CHARMM [Re: lennart]
prabhash Offline
Forum Member

Registered: 08/12/17
Posts: 10
Hi,
Rick
I am learner about CHARMM
When I the above gen_alpha_helix.inp
I got hte problem ! Unix environment variable CHM_HOME should point to the charmm installation directory
I am using the C43b1
what is the actual problem ?
what sequence should i follow for molecular dynamics simulation of the given above tar file examples
Regards,
ED

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