AMBER Archive (2004)

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

From: FyD (
Date: Fri Jan 23 2004 - 13:52:28 CST

Dear Ilyas,

> 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...

I guess you used such command in antechamber:
"antechamber -i job.log -fi gout -o job.pdb -fo mpdb -c resp"

In my opinion the PDB file generated by 'antechamber' (with the RESP charges in
it), can NOT be used in charges visualization in some graphic interfaces or
even directly used in MM simulation (I do not think that
'leap'/insightII/Sybyl/VMD can read charges from the PDB format, at least in
amber7 concerning 'leap'). To tell the truth, I even do not understand why the
RESP/ESP charges can be available in this PDB file (generated by antechamber)
because default PDB format does NOT have charges (see I guess it
is simply for information or this may change in xleap/amber8...

It is why in RED,, we decided to use the
Tripos format .mol2 where there is indeed a column for these charges in the
format ( Thus, with RED, after
structure optimization, MEP calculation and RESP fit, a Tripos structure 'can'
be generated with the optimized Cart. coordinates and charges. We do use such
.mol2 file to visualize the charges using insightII for instance
(Molecule/Label/Label_property = Partial_charge...). I guess it should also be
possible under Sybyl... 'xleap' can also visualize charges but I do not think
'xleap' can load Tripos format (or may-be in the new amber8 version...).

Regards, Francois

F.-Y. Dupradeau
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to