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
