I'm happy you've agreed with my idea.<br><br>The first step is you see the file aminoacids.rtp which contains all aminos that are supported by charmm in Gromacs. Furthermore, that file shows its atoms and bond length. <br>
<br>I've developed two kind of structure. First I've created some structures for mapping charmm parameters both amino and atoms. Second, I've created my topology global which contains the number of atoms and some other informations such as bond length for each pair of atoms as well as angle bond value. Basically, the second kind of structures work with int. The order way, the first kind work with type_atoms_t. <br>
<br>I believe you'll work only with the first kind of structures. All my structures are declared in topology_types.h (see [1]). <br><br>Feel free for comment or use of them. <br><br>[1] <a href="http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/topology_types.h">http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/topology_types.h</a><br>
<br>Thanks in advance,<br><br clear="all">--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>
Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br">http://laips.sel.eesc.usp.br</a><br>Phone: 55 (16) 3373-9366 Ext 229<br>Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218">http://lattes.cnpq.br/1025157978990218</a><br>
Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5">http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5</a><br>
<br><br><div class="gmail_quote">On Wed, Jul 21, 2010 at 5:34 PM, Sai Pooja <span dir="ltr"><<a href="mailto:saipooja@gmail.com">saipooja@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<div><br></div><div>So you mean it would be easier if one creates a topology file with all parameters obtained from charmm forcefield? </div><div>Yes, makes a lot more sense than trying to change the software. Can you give a little insight into the basic steps?</div>
<div><br></div><font color="#888888"><div>Pooja</div></font><div><div></div><div class="h5"><div><br></div><div><br><br><div class="gmail_quote">On Wed, Jul 21, 2010 at 1:43 PM, Rodrigo Faccioli <span dir="ltr"><<a href="mailto:rodrigo_faccioli@uol.com.br" target="_blank">rodrigo_faccioli@uol.com.br</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br><br>I've been developing an evolutionary algorithm which I would like to integrate it with Gromacs. Thus, in this moment, I'm updating my own code to attend the Gromacs patterns. <br>
<br>Based on charmm27.ff directory I've built h files which contain some amino acids (ALA, GLY and ARG). I'm modelling my algorithm I'll put more amino. However, if you want to see my files, please see the main in [1].<br>
<br>I create that file for mapping the files of charmm27.ff instead of work with .c files from pdb2gmx. Maybe if you create your charmm file mapping your job will be easier. <br><br>[1] <a href="http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/topology_charmm27_parameters.h" target="_blank">http://gitorious.org/protpred-gromacs/protpred-gromacs/blobs/master/include/topology_charmm27_parameters.h</a><br>
<br>Thanks in advance,<div><br><br clear="all">--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>
Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br" target="_blank">http://laips.sel.eesc.usp.br</a><br>Phone: 55 (16) 3373-9366 Ext 229<br>Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">http://lattes.cnpq.br/1025157978990218</a><br>
Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5" target="_blank">http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5</a><br>
<br><br></div><div><div></div><div><div class="gmail_quote">On Wed, Jul 21, 2010 at 1:38 PM, Sai Pooja <span dir="ltr"><<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks Rodrigo. I have read the paper and and I am familiar with the topology folder. <div>This is what I want to do:</div><div><br></div><div>I have a version of gromacs without the charmm forcefield which I have modified to use an algorithm I need. </div>
<div><br></div><div>However, I now need to use charmm ff with this algorithm and in gromacs. </div><div><br></div><div>It would be extremely tedious to modify another version of gromacs(with charmm ff i.e.) for this algorithm. So , I was thinking if I could just copy the top folder from a git version of gromacs(with charmmff) and make changes in configure files to make it work with my version?</div>
<div><br></div><div>Can someone give me some pointers on this? For example which files much be changed/ modified?</div><div><br></div><div>I have some thoughts:</div><div>1. Clearly, the topology folder has been changed. It has new files on charmm and the organization of files has also been changed --> cp topology folder from git and put into my version</div>
<div><br></div><div>2. Make changes in <a href="http://configure.ac" target="_blank">configure.ac</a> </div><div>The git version have extra commands for compiling top files for each forcefield - copy those commands exactly from the git version and add to my version.</div>
<div><br></div><div>3. I think that some files connected to pdb2gmx might have to be changed. Which ones I am not sure. I am only interested in the .c files. Maybe toppush.c?</div><div><br></div><div>What else would I need to change? Any pointers would be very helpful. Kindly let me know even if you have attempted something similar.</div>
<div><br></div><div>Thanks</div><div>Pooja</div><div><div></div><div><div><br></div><div><div class="gmail_quote">On Tue, Jul 20, 2010 at 8:14 PM, Rodrigo Faccioli <span dir="ltr"><<a href="mailto:rodrigo_faccioli@uol.com.br" target="_blank">rodrigo_faccioli@uol.com.br</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br><br>The gromacs version in git master, please see the directory share/top/charmm27.ff<br>
<br>That directory contains whole gromacs charmm files. Furthermore, please see the reference below which explain more details about these parameters.<br>
<br>Bjelkmar, Larsson, Cuendet, Hess, and Lindahl, JCTC 2010<br><br>I hope those informations help you.<br><br>What do you want to do more specific?<br><br clear="all">--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>
University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br" target="_blank">http://laips.sel.eesc.usp.br</a><br>
Phone: 55 (16) 3373-9366 Ext 229<br>Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218" target="_blank">http://lattes.cnpq.br/1025157978990218</a><br>Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5" target="_blank">http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5</a><br>
<br><br><div class="gmail_quote"><div><div></div><div>On Tue, Jul 20, 2010 at 6:57 PM, Sai Pooja <span dir="ltr"><<a href="mailto:saipooja@gmail.com" target="_blank">saipooja@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div>
Hi,<div><br></div><div>If one has to make a version of gromacs charmm compatible, which files from the charmm compatible version must be looked at?</div><div><br></div><div>Pooja<br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
</div>
<br></div></div>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
</div>
</div></div><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>
</div></div><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Quaerendo Invenietis-Seek and you shall discover.<br>
</div>
</div></div><br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>