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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Received on Thu Jul 07 2011 - 11:30:03 PDT
