[gmx-users] A simple question

[saeed poorasad]

Can you please let me know what the problem is ? 
      From: saeed poorasad <s_poorasad at yahoo.com>
 To: "Smith, Micholas D." <smithmd at ornl.gov>; "gmx-users at gromacs.org" <gmx-users at gromacs.org> 
 Sent: Tuesday, 14 April 2015, 9:59
 Subject: Re: [gmx-users] A simple question
   
Dear Dr.Smith ,
Thanks for your replay .
This is a part of my PDB file : 
ATOM      1  CD1 TRP      1      19.910  19.430  16.500  1.00  0.00ATOM      2  CD1 TRP      1      20.210  20.850  16.560  1.00  0.00ATOM      3  CD1 TRP      1      19.010  21.540  16.970  1.00  0.00ATOM      4  CD1 TRP      1      17.960  20.560  17.150  1.00  0.00ATOM      5  CD1 TRP      1      18.520  19.250  16.860  1.00  0.00ATOM      6  CD1 TRP      1      19.090  22.640  17.820  1.00  0.00...I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field.

Best regards ,Saeed.



 
 

     From: "Smith, Micholas D." <smithmd at ornl.gov>
 To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>; saeed poorasad <s_poorasad at yahoo.com> 
 Sent: Monday, 13 April 2015, 21:24
 Subject: Re: [gmx-users] A simple question
   
Hi Saeed,

Attachments don't work with the mailing list. Could you copy a few lines of the pdb for us to look at and maybe upload the pdb you generated to dropbox or a similar site?

Also pdb2gmx may not be the best route here. You may need to explicitly write your own topology file (tedious as it may be), but lets take a closer look at what your pdb first.

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of saeed poorasad <s_poorasad at yahoo.com>
Sent: Monday, April 13, 2015 2:29 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] A simple question

Hi .
Dear Gromacs users .
Today is the first day that i am working with GROMACS .I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field.
Can you please let me know what the problem is ?
I have attached my PDB file with this Email.
Best ,Saeed.