<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
<title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
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:<br>
<br>
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:<br>
<br>
editconf -f sedoheptulose.gro.pdb -o sedoheptulose.cube.pdb -bt cubic
-d 2.0<br>
genbox -cp sedoheptulose.cube.pdb -cs spc216.gro -o
sedoheptulose.water.pdb -p sedoheptulose.top -nice 0<br>
grompp -np 1 -f em.mdp -c sedoheptulose.water.pdb -p sedoheptulose.top
-o sedoheptulose.em.tpr<br>
<br>
but in the grompp commands the following error occurs:<br>
<br>
-------------------------------------------------------<br>
Program grompp, VERSION 3.3.1<br>
Source code file: topio.c, line: 388<br>
<br>
Fatal error:<br>
Invalid order for directive moleculetype, file ""sedoheptulose.top"",
line 17<br>
-------------------------------------------------------<br>
<br>
but in line 17 only "[ moleculetype ]" is written?<br>
<br>
<br>
<br>
in the second case I do not really understand the error message:<br>
<br>
x2top -f sedoheptulose.pdb -o sedoheptulose.top<br>
<br>
leads to:<br>
<br>
-------------------------------------------------------<br>
Program x2top, VERSION 3.3.1<br>
Source code file: futil.c, line: 537<br>
<br>
Fatal error:<br>
Library file ffG43a1.n2t not found in current dir nor in default
directories.<br>
(You can set the directories to search with the GMXLIB path variable)<br>
-------------------------------------------------------<br>
<br>
<br>
also in the faq i could not find a real guide how to simulate such a
molecule ...<br>
<br>
<br>
<br>
Bernhard<br>
<br>
<br>
<br>
<br>
[1] <a class="moz-txt-link-freetext" href="http://davapc1.bioch.dundee.ac.uk/prodrg/index.html">http://davapc1.bioch.dundee.ac.uk/prodrg/index.html</a><br>
<br>
<br>
<br>
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> wrote:
<blockquote cite="mid20081119142346.60B4F244F8@struktbio205.bmc.uu.se"
type="cite">
<pre wrap="">
Message: 1
Date: Wed, 19 Nov 2008 13:25:07 +0000
From: "Kukol, Andreas" <a class="moz-txt-link-rfc2396E" href="mailto:a.kukol@herts.ac.uk"><a.kukol@herts.ac.uk></a>
Subject: RE: [gmx-users] sedoheptulose
To: Discussion list for GROMACS users <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a>
Message-ID:
<a class="moz-txt-link-rfc2396E" href="mailto:2F848DC922C8D741BF3A60B7D7108B6A7C6BD2D23B@UH-MAILSTOR.herts.ac.uk"><2F848DC922C8D741BF3A60B7D7108B6A7C6BD2D23B@UH-MAILSTOR.herts.ac.uk></a>
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.
<a class="moz-txt-link-freetext" href="http://wiki.gromacs.org/index.php/FAQs">http://wiki.gromacs.org/index.php/FAQs</a>
x2top and the prodgr web-server might be some good starting points.
Andreas
</pre>
<pre wrap=""><!---->From: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>] On Behalf Of Bernhard Knapp
Sent: 19 November 2008 12:54
To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
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
</pre>
</blockquote>
</body>
</html>