Re: Software for molecular electrostatic calculations

From: Rabeta Yeasmin (rabetayeasmin_at_gmail.com)
Date: Thu Aug 10 2017 - 10:31:58 CDT

Dear Mr. Fiorin,

I have tried to use their web server. But it is showing -
404
file not found.

I am wondering how can I use their web server.
Thanks.

Rabeta Yeasmin

On Thu, Aug 10, 2017 at 8:15 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Please read the doc from the APBS website.
>
> On Wed, Aug 9, 2017 at 5:44 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
> wrote:
>
>> Dear Mr. Fiorin,
>>
>> Thanks very much for your correction. I am wondering how can I use APBS.
>> Do I need to install it or I can use web server of it?
>>
>> Regards
>> Rabeta Yeasmin
>>
>> On Wed, Aug 9, 2017 at 2:16 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> wrote:
>>
>>> There are several, but of those I tried APBS has the cleanest user
>>> interface in my opinion. Note that the electrostatic potential will only
>>> measure unscreened charges, but not the hydrophobic effect:
>>> https://en.wikipedia.org/wiki/Hydrophobic_effect
>>> because it is not due only to electrostatics.
>>>
>>> Giacomo
>>>
>>> On Wed, Aug 9, 2017 at 2:03 PM, Rabeta Yeasmin <rabetayeasmin_at_gmail.com>
>>> wrote:
>>>
>>>> Dear NAMD Users,
>>>>
>>>> I want to calculate molecular electrostatic potential and create a
>>>> electrostatic map showing hydrophobic and hydrophilic part. I believe APBS
>>>> is one of the software which can do this. I am wondering if anyone can
>>>> suggest me any other software like APBS. I have searched on line and found
>>>> some like Delphi Tools, UHBD, PBEQ solver, Avagadro and Jmol. I am not sure
>>>> if they can perform the same thing as APBS. If anyone is familiar which
>>>> these tools, please give me some idea and suggestions.
>>>>
>>>> Thanks.
>>>>
>>>> Regrads
>>>> Rabeta Yeasmin
>>>>
>>>
>>>
>>>
>>> --
>>> Giacomo Fiorin
>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>> Contractor, National Institutes of Health, Bethesda, MD
>>> http://goo.gl/Q3TBQU
>>> https://github.com/giacomofiorin
>>>
>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:30 CST