Re: [apbs-users] apbs-users Digest, Vol 100, Issue 8

[Arnab Nayek]

Hi,

   I think APBS works only in implicit solvent condition. So when u convert PDB file to PQR file by PDB2PQR it only takes the atomic coordinates not the hetero atoms coordinates. When you prepare the input file for APBS u have to set the values of dielectric constants of water (default - 80) and protein (default - 4) for implicit solvation, u don't need to add solvent explicitly.

Thanking you.

Arnab Nayek

On Fri, Nov 21, 2014 at 7:02 AM, <apbs-user...@lists.sourceforge.net> wrote:

Send apbs-users mailing list submissions to
        apbs-...@lists.sourceforge.net

To subscribe or unsubscribe via the World Wide Web, visit
        https://lists.sourceforge.net/lists/listinfo/apbs-users
or, via email, send a message with subject or body 'help' to
        apbs-user...@lists.sourceforge.net

You can reach the person managing the list at
        apbs-use...@lists.sourceforge.net

When replying, please edit your Subject line so it is more specific
than "Re: Contents of apbs-users digest..."


Today's Topics:

   1.  Eplicit solvent (Roy Assis)


----------------------------------------------------------------------

Message: 1
Date: Tue, 18 Nov 2014 06:09:23 -0800 (PST)
From: Roy Assis <roya...@gmail.com>
Subject: [apbs-users] Eplicit solvent
To: apbs-...@googlegroups.com
Message-ID: <e4324056-8a9c-484f...@googlegroups.com>
Content-Type: text/plain; charset="utf-8"

Hello

I'm trying to run APBS for a pdb file of a protein with an explicit
solvent. The file was created using GROMACS.

I don't have alot of knowledge in the issue, I was wandering if 1) APBS can
make such calculations and 2) How do I make a PQR from my PDB (that
includes water), the pdb2pqr server does not support water to my
understanding, and is ommiting them during the charge assignment.
Finally, 3), does APBS with explicit solvent (generated during an MD run)
is more reliable with APBS with implicit solvent (that include
a-priori assumptions).

Thank you
Roy
-------------- next part --------------
An HTML attachment was scrubbed...

------------------------------

------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk

------------------------------

_______________________________________________
apbs-users mailing list
apbs-...@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/apbs-users


End of apbs-users Digest, Vol 100, Issue 8
******************************************