[gmx-users] sedoheptulose

[Bernhard Knapp]

thanks for the hints but unfortunately i still can not get the molecule 
running. i tried with both prodrg server and x2top but with limited success:

in the first case i generate the gro.pdb and .top file via the 
webinterface [1] of prodrg by pasting my coordinate file into the 
textbox. then i run the following commands:

editconf -f sedoheptulose.gro.pdb -o sedoheptulose.cube.pdb -bt cubic -d 2.0
genbox -cp sedoheptulose.cube.pdb -cs spc216.gro -o 
sedoheptulose.water.pdb -p sedoheptulose.top -nice 0
grompp -np 1 -f em.mdp -c sedoheptulose.water.pdb -p sedoheptulose.top 
-o sedoheptulose.em.tpr

but in the grompp commands the following error occurs:

-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: topio.c, line: 388

Fatal error:
Invalid order for directive moleculetype, file ""sedoheptulose.top"", 
line 17
-------------------------------------------------------

but in line 17 only "[ moleculetype ]" is written?



in the second case I do not really understand the error message:

x2top -f sedoheptulose.pdb -o sedoheptulose.top

leads to:

-------------------------------------------------------
Program x2top, VERSION 3.3.1
Source code file: futil.c, line: 537

Fatal error:
Library file ffG43a1.n2t not found in current dir nor in default 
directories.
(You can set the directories to search with the GMXLIB path variable)
-------------------------------------------------------


also in the faq i could not find a real guide how to simulate such a 
molecule ...



Bernhard




[1] http://davapc1.bioch.dundee.ac.uk/prodrg/index.html



gmx-users-request at gromacs.org wrote:

>Message: 1
>Date: Wed, 19 Nov 2008 13:25:07 +0000
>From: "Kukol, Andreas" <a.kukol at herts.ac.uk>
>Subject: RE: [gmx-users] sedoheptulose
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID:
>	<2F848DC922C8D741BF3A60B7D7108B6A7C6BD2D23B at UH-MAILSTOR.herts.ac.uk>
>Content-Type: text/plain; charset="iso-8859-1"
>
>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
>
>
>  
>
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