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#18819 - 09/03/08 10:51 AM Solvent accessible area script and radial distribution script
Lingling_Shen Offline
Forum Member

Registered: 09/02/08
Posts: 5
Dear all:

I am a new user. I have a finished simulation and I have all the output trjectory files (*.dcd). I am wondering, for the whole trajectory file, how I can calculate the total SAS for the selected atoms, and g(r) of water proton whithin certain distance away from selected atoms - selected atoms.

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#18820 - 09/03/08 10:58 AM Re: Solvent accessible area script and radial distribution script [Re: Lingling_Shen]
lennart Online   content

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Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E
See Sample scripts for basic tasks in CHARMM in the Script Archive for an example of SAS (ASA) calculation. RDFs are described with examples in corman.doc (coor anal ....).
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#18821 - 09/03/08 03:38 PM Re: Solvent accessible area script and radial distribution script [Re: lennart]
Lingling_Shen Offline
Forum Member

Registered: 09/02/08
Posts: 5
Thanks.
I am using the MD output from Discovery Studio. I am running nucleotide simulation. I am trying to use your rgyr script to calculate radial distribution. This is my script:
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stream "ModelBuild.stream"

STREAM "noneSolvation.stream"

STREAM "nonbond.stream"

read coor card name T10_3N_single_prod.crd

open unit 51 read unform name T10_3N_single_prod.dcd

open unit 21 read unform name @9pept500.cor
open unit 31 write form name @9pept500.gonh
coor anal select type HT end - ! Water oxygens
site select type NT end multi - ! and the amide hydrogens
firstu 1 nunit 1 skip 10 - ! trajectory specification
isdist 31 - ! do the g(r) (here solute-solvent)
mgn 100 dr 0.1 - ! comp. g(r) at MGN points separated by DR
rdsp 2.5 -
rsph 999.9 - ! we use ALL waters for the calculation
xbox @6 ybox @7 zbox @8 ! and we did use PBC


-------------
It does not work. I am wondering what is wrong?
Thanks,

-L


Attachments
18989-test.txt (696 downloads)


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#18822 - 09/03/08 04:25 PM Re: Solvent accessible area script and radial distribution script [Re: Lingling_Shen]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4741
Loc: ~ 59N, 15E

1. Read the error message - you have some kind of problem with your basic setup, in particlar with the topology/parameter files. It usually (read: always) is important to pay close attention to the first error message. When you want (free) help from others, do not hide the error message in an attachment.
You have not yet reached the part of the problem you asked about in the first place.
2. You have a commercial version of CHARMM, and thus you have the privilege of commercial support via Accelrys - use it, your company has probably paied real money for it!
3. The stream commands to unknown files makes it difficult to judge the quality of your input.
4. Still there are several inconsistencies in your input. Do you actually intend to read a trajectory contained in the file named pept500.cor? And what does the variable @9 represent in this command?
"open unit 21 read unform name @9pept500.cor"

!Innocent, but what makes you think that "type HT" refers to water oxygens?
coor anal select type HT end - ! Water oxygens
!Recheck "type NT"
site select type NT end multi - ! and the amide hydrogens
!What file did you open for reading on unit 1, referenced below?
firstu 1 nunit 1 skip ...
!RDSP 2.5???
!Did you use Periodic Boundary Conditions (of the simple type supported by this CHARMM command)? What about variables 6,7, and 8?

I hope the above helps you formulating good questions to Accelrys support!
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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