[apbs-users] confusion for calculation setup

[Abhishek TYAGI]

Dear Experts,

I am new to APBS calculation.

What I have is as follows:

1. I am working on ubuntu OS, and installed pdb2pqr and apbs using apt-get install command, and tried running them, and it seems it is running perfectly.

2. I had finished MD using namd, therefore I have pdb, psf and dcd file for protein and graphene system for 100 ns. 

3. Now, I would like to calculate the energy between protein and graphene. I noticed that in CHARMM.dat/names file have force field parameters for proteins, although for graphene sheet I have modified the files, I am not sure it is correct, please suggest:

for dat file: 

GRA CG 0.00 1.992400  CG1

GRA CG1 0.00 1.992400  CG

GRA C 0.00 1.992400  CG

for names file:

   </residue>

    <residue>

        <name>GRA</name>

        <atom>

            <name>C</name>

            <useatomname>CG</useatomname>

        </atom>

        <atom>

            <name>CG</name>

            <useatomname>CG1</useatomname>

        </atom>

    </residue>

4. Now using this file i tried to convert the pdb to pqr format, and pdb2pqr says, file converted sucessfully. 

5. My confusion is to how to setup next step for the calculation, to obtain the enrgy w.r.t time scale.

SHould I have to remove water and ions from the MD system, and the use the dry system for calculations, i think i need to export three files (a) nothing but protein, (b) nothing but graphene, (c) only protein and graphene together, and there dcd files. However, I am not sure how to proceed.

Please sugget how to proceed, its important to understand.

Thanks in advance.  

Abhi

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

[Abhishek TYAGI]

Dear All,

Any suggestions?

Thanks

Abhi

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

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From: Abhishek TYAGI <atya...@connect.ust.hk>
Sent: Saturday, October 15, 2016 12:45:40 AM
To: apbs-...@lists.sourceforge.net
Subject: [apbs-users] confusion for calculation setup

 

[Baker, Nathan]

Hello –

 

I’ve Cc’ed Dave, Keith, and Juan for their help.

 

Thank you,

 

--

Nathan Baker

Advanced Computing, Mathematics, and Data Division — Pacific Northwest Natl Lab

Division of Applied Mathematics — Brown University

+1-509-375-3997 — http://go.usa.gov/xWY9Y