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#718 - 12/15/03 09:25 AM Tools and scripts for CHARMM use
charlesbrooks Offline

Forum Member

Registered: 12/15/03
Posts: 92
Please see the web pages off http://mmtsb.scripps.edu for the MMTSB Toolset and associated scripts and tutorials to use CHARMM.

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#719 - 04/05/05 02:51 AM Re: Tools and scripts for CHARMM use [Re: charlesbrooks]
Leonardo Offline
Forum Member

Registered: 03/17/05
Posts: 42
Loc: Chile-Santiago
Hello Dr. Brooks.

I want to compute the contact map for every frame of a dynamics trayectory (or a subset), to obtain:
1) a residue profile with the number of contacts made by each residue
2) the number of NATIVE and NON-NATIVE contacts for each residue
3) the contact matrix for each conformation.

I searched in your MMTSB webpage and I found CONTACT.pl. Nevertheless, it uses a one tipe cutoff to calculate the contacts. I would like to calculate a contact between atoms A and B using an atom-defined cutoff, as Rvdw(A) + Rvdw(B) + r, where r can be a user-defined cutoff. I would like to ask you where can I found the wdwradii for each atom for param22 (and other FF) to make those calculations, and which would be a good method to extract a Human-readable coordinate-pdb-like file from a dcd trayectory to calculate those things.

Or better, if there is a script to do that already.

Best regards

Leonardo
_________________________
Leonardo Sepulveda Durán Universidad de Chile

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#720 - 09/07/05 12:57 AM Re: Tools and scripts for CHARMM use [Re: Leonardo]
charlesbrooks Offline

Forum Member

Registered: 12/15/03
Posts: 92
Please look at examples in the corman.doc for examples of computing contact maps.

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#28535 - 10/23/11 12:49 AM Re: Tools and scripts for CHARMM use [Re: charlesbrooks]
RAJIV KUMAR KAR Offline
Forum Member

Registered: 09/01/11
Posts: 22
Hello Dr. Brooks

I want to add counter ions to the DNA system for neutralization at specific distance, and not by randomly replacing the water molecules.

can i do it by using MMTSB toolset.

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