Re: [AMBER] APBS

From: Robert Konecny <rok.ucsd.edu>
Date: Thu, 7 Jul 2011 11:17:22 -0700

Hi Dan,

in the simplest case you just need your .prmcrd and .prmtop files. The APBS
PB solver will use charge and radius information from your prmtop file. See
iapbs/modules/Amber/test/Visualization directory in the iAPBS distribution
for examples.

You could also read in charge and radius information from an external PQR
file, see the radiopt and pqr keywords:
http://mccammon.ucsd.edu/iapbs/usersguide/using-amber.html.

Best,

Robert

On Thu, Jul 07, 2011 at 02:05:07PM -0400, Daniel Aiello wrote:
> Hi Robert,
>
> Thanks for the advice. The input files in example 5.1.4 are for
> sander.APBS. I am still unclear as to what the other input files should
> be passed to sander.APBS. At this point we have run our MD simulations
> and have a trajectory of standard sander MD snapshots. How does
> sander.APBS deal with these? Thanks a bunch for any info you can
> provide, Dan On Jul 7, 2011, at 1:48 PM, Robert Konecny wrote:
>
> > Hi Dan,
> >
> > as far as generating APBS electrostatic maps from MD simulations: you could
> > do what you are proposing - getting the structures from MD using ptraj then
> > running pdb2pqr and APBS to get the potential maps. But since you already
> > have sander.APBS you could do all this directly from sander. sander.APBS
> > can write out the potential maps for the given structure in DX format for
> > you. You could even run an MD simulation and have sander.APBS write out
> > elstat potential maps every n-th step.
> >
> > If you are interested in only getting elstat potential maps from your final
> > structures - please take a look at example 5.1.4 from the iAPBS user guide
> > http://mccammon.ucsd.edu/iapbs/usersguide/examples-amber.html. This shows
> > how to set up such a calculation.
> >
> > Best,
> >
> > Robert
> >
> > On Fri, Jul 01, 2011 at 10:06:23AM -0400, Daniel Aiello wrote:
> >> Hello, We are using amber10 to simulate protein receptor-ligand
> >> complexes. We would like to visualize the electrostatic potential of
> >> these complexes. APBS seems to be a good option for generating
> >> electrostatic maps to be used as input for any number of molecular
> >> visualization software, we will most likely use jmol. I have compiled
> >> APBS, iAPBS, and sander.APBS. I've tried to compute binding energies
> >> with mm_pbsa.pl and APBS as the alternative PB solver. It appears to be
> >> working but my statistics.out file is empty and running the calculation
> >> manually with mm_pbsa_statistics.pl does not work. After reading
> >> documentation, I'm still not sure what the output files are supposed to
> >> contain when using mm_pbsa.pl with APBS? I'm not even sure I need to run
> >> sander.APBS in order to generate electrostatic maps. Also, I'm unclear
> >> on the methods for generating electrostatic maps with APBS for our
> >> simulations? I'm thinking of computing an average structure with ptraj,
> >> preparing this structure with PDB2PQR for electrostatic s calcs, and then
> >> using APBS to generate an electrostatic map of this structure. I guess I
> >> am confused about the workflow involved in generating electrostatic maps
> >> from MD simulations. Any insight would be appreciated? Thanks, Dan
> >>
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>
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Received on Thu Jul 07 2011 - 11:30:04 PDT
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