[gmx-users] sedoheptulose

[Kukol, Andreas]

Yes, it is possible by deveoping your own topology. Pdb2gmx is not suitable for that purpose.

It would be helpful to check out the documentation resources and manual, e.g.

http://wiki.gromacs.org/index.php/FAQs

x2top and the prodgr web-server might be some good starting points.

Andreas

>>>>>
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Bernhard Knapp
Sent: 19 November 2008 12:54
To: gmx-users at gromacs.org
Subject: [gmx-users] sedoheptulose

Dear users

I would like to perform a MD simulation of Sedoheptulose (C7H14O7) via Gromacs. But already during pdb2gmx it comes up with:
"Residue 'UNK' not found in residue topology database" which is obviously clear since sedoheptulose is not an amino acid. Is it somehow possible to simulate this molecule?

the sedoheptulose data to start from is:
ATOM      1  C   UNK     0      -3.442   2.742   0.000  0.00  0.00           C+0
ATOM      2  C   UNK     0      -2.108   3.512   0.000  0.00  0.00           C+0
ATOM      3  C   UNK     0      -0.774   2.742   0.000  0.00  0.00           C+0
ATOM      4  C   UNK     0       0.559   3.512   0.000  0.00  0.00           C+0
ATOM      5  C   UNK     0       1.893   2.742   0.000  0.00  0.00           C+0
ATOM      6  C   UNK     0       3.227   3.512   0.000  0.00  0.00           C+0
ATOM      7  O   UNK     0      -0.774   1.202   0.000  0.00  0.00           O+0
ATOM      8  O   UNK     0       0.559   5.052   0.000  0.00  0.00           O+0
ATOM      9  O   UNK     0       1.893   1.202   0.000  0.00  0.00           O+0
ATOM     10  O   UNK     0      -4.775   3.512   0.000  0.00  0.00           O+0
ATOM     11  O   UNK     0      -2.108   5.052   0.000  0.00  0.00           O+0
ATOM     12  H   UNK     0      -6.109   2.742   0.000  0.00  0.00           H+0
ATOM     13  H   UNK     0      -0.774   5.822   0.000  0.00  0.00           H+0
ATOM     14  H   UNK     0       1.893   5.822   0.000  0.00  0.00           H+0
ATOM     15  H   UNK     0       0.559   0.432   0.000  0.00  0.00           H+0
ATOM     16  H   UNK     0       3.227   0.432   0.000  0.00  0.00           H+0
ATOM     17  C   UNK     0       4.560   2.742   0.000  0.00  0.00           C+0
ATOM     18  O   UNK     0       5.894   3.512   0.000  0.00  0.00           O+0
ATOM     19  H   UNK     0       7.228   2.742   0.000  0.00  0.00           H+0
ATOM     20  O   UNK     0       3.227   5.052   0.000  0.00  0.00           O+0

cheers
bernhard