<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks a lot for your mail.<br>I hope it will help me.<br>Regards<br><br><br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Sat, 27/3/10, durmaz@zib.de <i><durmaz@zib.de></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: durmaz@zib.de <durmaz@zib.de><br>Subject: Re: [gmx-users] query regarding atom type<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Saturday, 27 March, 2010, 8:56 PM<br><br><div class="plainMail">hi there,<br><br>i'm doing simulation of protein-ligand systems since a few weeks and i've<br>been starting with a nice tutorial for acpypi (python script)<br><br><a href="http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs" target="_blank">http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs</a><br><br>in order to
create topology-files for several (42) ligands in an automized<br>way. works very fine so far.<br><br>changes, that i've applied to the tutorial: i don't add water at the<br>pdb2gmx step, but only later at the genbox step. in addition, i add the<br>include line for the water topology "manually" (script). however, if you<br>use acpypi, you should remove the coordinates/topology (section [<br>moleculetype ], [ atoms ], [ bonds ], ...) of the protein from the<br>protein.top (generated by pdb2gmx) and create a own protein.itp file<br>containing that information, which than needs to be included in the<br>protein.top file.<br><br>restriction on acpypi: number of ligand's atoms is limited to about 200<br>(not sure).<br><br>regards,<br><br>vedat<br><br><br>> Hello All<br>> I am trying to add ions to my protein, for that I have run this command,,<br>><br>> [sakshi@localhost ~/sonali]$ grompp -f ions.mdp -c protein_solv.gro -p<br>> topol.top
-o ions.tpr<br>> and every time I run it, following error is coming<br>> Fatal error:<br>> Atomtype OA not found<br>><br>> I am using OPLSA force field and I have a ligand in my molecule in which<br>> this atom type is there.<br>> I have tried to change the atom type after seeing force field's .itp file<br>> and<br>> I have also included ligand .itp file in topology file.<br>> But nothing is working for me.<br>><br>> Please help<br>> Thanks in advance<br>><br>><br>><br>> --<br>> Sonali Dhindwal<br>><br>><br>> Your Mail works best with the New Yahoo Optimized IE8. Get it NOW!<br>> <a href="http://downloads.yahoo.com/in/internetexplorer/--" target="_blank">http://downloads.yahoo.com/in/internetexplorer/--</a><br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org"
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