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Dear Outi,<br>
I have the same problem some time ago.<br>
What I did then was to generate the topology with PRODRG for GROMOS87
and then convert it to GROMOS96 by hand (you have to use the
paramenters in the itp file of GROMOS87/96). It´s really tedious but it
works<br>
Hope this help<br>
Good luck!<br>
Regards<br>
Ruben<br>
Daan van Aalten wrote:<br>
<blockquote type="cite"
cite="midPine.LNX.4.33.0309231324510.535-100000@davapc1.bioch.dundee.ac.uk">
<pre wrap="">you cannot use the PRODRG topologies with anything else than the ffgmx
force field
On Mon, 22 Sep 2003, Outi Maija Salo wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi!
We have some problems in preparing a normal MD run for a protein-ligand
complex.
We prepared the ligand .itp and .gro files in PRODRG server.
THen we added these files to corresponding .gro file and .top file of the
protein just as we have previously done and it worked then.
We chose to use the GROMOS96(ffG43a1) force field (this was new to
previous work).
The first problem occurred when we tried to use grompp:
Fatal error: Atomtype 'CR61' not found!
Well, this atom type was not in ffG43a1.atp. So, we changed this and some
other atom types to the corresponding types of this force field.
Our ligand has the name LIG.
The next error message from grompp was the following:
WARNING 2 [file "top_ligand.top", line 18689]:
atom C35 (Res LIG-301) has mass 0
WARNING 3 [file "top_ligand.top", line 18689]:
atom C34 (Res LIG-301) has mass 0
WARNING 4 [file "top_ligand.top", line 18689]:
atom C33 (Res LIG-301) has mass 0
WARNING 5 [file "top_ligand.top", line 18689]:
atom O36 (Res LIG-301) has mass 0
WARNING 6 [file "top_ligand.top", line 18689]:
atom HAA (Res LIG-301) has mass 0
WARNING 7 [file "top_ligand.top", line 18689]:
atom C32 (Res LIG-301) has mass 0
WARNING 8 [file "top_ligand.top", line 18689]:
atom C31 (Res LIG-301) has mass 0
WARNING 9 [file "top_ligand.top", line 18689]:
atom C30 (Res LIG-301) has mass 0
WARNING 10 [file "top_ligand.top", line 18689]:
atom C29 (Res LIG-301) has mass 0
...
What is the problem? Is the GROMOS96 ff not suitable for protein-ligand
complexes or should we change some ff parameters e.g. in ffG43a1nb.itp
file? We really could not find the reason for this...
Thanks for your help!
Outi Salo
University of Kuopio
Finland
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</pre>
</blockquote>
<pre wrap=""><!---->
##############################################################################
Dr. Daan van Aalten Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764
School of Life Sciences E-mail: <a class="moz-txt-link-abbreviated" href="mailto:dava@davapc1.bioch.dundee.ac.uk">dava@davapc1.bioch.dundee.ac.uk</a>
Univ. of Dundee, Dundee DD1 5EH, UK WWW: <a class="moz-txt-link-freetext" href="http://davapc1.bioch.dundee.ac.uk">http://davapc1.bioch.dundee.ac.uk</a>
O C O C Visit the PRODRG server to take
" | " | the stress out of your topologies!
N--c--C--N--C--C--N--C--C--N--C--C--O
| " | <a class="moz-txt-link-rfc2396E" href="http://davapc1.bioch.dundee.ac.uk/C-C-OOC-C-COprograms/prodrg/prodrg.html">" http://davapc1.bioch.dundee.ac.uk/
C-C-O O C-C-C O programs/prodrg/prodrg.html
"</a>
O
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</pre>
</blockquote>
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