Re: AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7

From: Joey Harriman <>
Date: Fri, 23 Jan 2004 14:43:43 -0400

Hi Ilyas,

Are you sure that you have charges on your molecule. Typically, pdb files don't have
charges (unless it's a pdbq file or something like this). Try using a tripos file
(mol2) or an antechamber prep file (*.ac ). Here is the methodology that I use to get
RESP charges from a Gaussian output:

$ antechamber -i name.out -fi gout -o name.mol2 -fo mol2 -nc [] -c resp -at amber

Look at the mol2 (could also use an antechamber prep file) text file to see if the
charges are in the data file. I think that you should be able to load the charges and
view them in xleap. Any MM program should be able to show you the charges in the
tripos file. These include MOE, MacroModel, MM2, etc.... Good luck.


Quoting Ilyas Yildirim <>:

> Dear AMBER Members,
> I am new in using AMBER 7, and I need to calculate the RESP charges for a
> specific nucleic acid molecule. After using the G98 to minimize the
> structure and to find the ESP charges in a HF/6-31G(d) field-basis set,
> and then using 'antechamber' to get the RESP charges, I got the *.pdb
> file. (It was automatically created by antechamber) I want to visualize
> this pdb file such that I can see the RESP Charges next to each
> corresponding atom. I have used the VMD, but it seems that there is no
> command to put these RESP charges next to each corresponding atom. Can you
> give me any suggestions how to do this? It is possible to put the charges
> by first getting a picture of the molecule, and using ADOBE Photoshop to
> write down the charges seperately, but it will take some time of me. Any
> suggestions are welcome and thanks in advance...
> --
> Ilyas Yildirim
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Joey Harriman
MSc Computational Chemistry
University of New Brunswick
Room 228
Toole Hall

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Received on Fri Jan 23 2004 - 18:53:01 PST
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