Hi All/Justin,<br> I got the *.atp file from Mark Abraham and now it is not complaining about ON2b atom type. But now I am getting the following error while I was trying to create *.top file using the command: /Users/parimalkar/gromacs-4.0.5/bin/pdb2gmx_d -ff charmm -f step5_assembly.pdb -p topol.top -o dopc.pdb <br>
<br>Program pdb2gmx_d, VERSION 4.0.5<br>Source code file: ter_db.c, line: 87<br><br>Fatal error:<br>Reading Termini Database: expected 3 items of atom data in stead of 1 on line<br> N NH3 14.0027 -0.3000<br>
-------------------------------------------------------<br><br>Please help me !<br>Thanks<br>Chanchal<br><br><br><div class="gmail_quote">On Tue, Sep 29, 2009 at 11:42 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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;"><br>
<br>
Chanchal 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 All,<br>
I am have built a DOPC+water (tip3p) system in <a href="http://www.charmm-gui.org" target="_blank">www.charmm-gui.org</a> <<a href="http://www.charmm-gui.org" target="_blank">http://www.charmm-gui.org</a>>. I converted *.itp file from CHARMM *.prm file using Mark Abraham's script. I placed these *.itp files into the GMXLIB directory. I have also edited FF.dat file and add a line "ffcharmm CHARMM 27" and updated the line number. Now when I execute the command: /Users/parimalkar/gromacs-4.0.<div>
<div></div><div class="h5"><br>
5/bin/pdb2gmx_d -ff charmm -f step5_assembly.pdb -p topol.top, I got the error message<br>
"Fatal error:<br>
Library file ffcharmm.atp not found in current dir nor in default directories.<br>
<br>
(You can set the directories to search with the GMXLIB path variable)"<br>
<br>
<br>
<br>
Now when I copied the ffcharmm27.atp to ffcharmm.atp, and executed the same command, then I got the error message:<br>
<br>
<br>
Program pdb2gmx_d, VERSION 4.0.5<br>
Source code file: resall.c, line: 138<br>
<br>
Fatal error:<br>
Atom type ON2b (residue TP1) not found in atomtype database<br>
<br>
But I saw that ffcharmm.rtp (Yuguang Mu's file that I got from Mark Abraham) contains ON2b. So how can I fix this error? Is it problem with ffcharmm.atp? Should I not copy ffcharmm27.atp to ffcharmm.atp?<br>
<br>
</div></div></blockquote>
<br>
The atomtype database is the .atp file, not the .rtp. If the atom does not appear in the .atp file, you won't be able to use that type without defining parameters for it.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thanks<br>
Chanchal<br>
<br>
<br>
------------------------------------------------------------------------<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 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>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<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 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>