OK. I'll take a look. Thanks,
Dan
On Jul 7, 2011, at 2:17 PM, Robert Konecny wrote:
> 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 - 11:30:05 PDT
