<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">I am sorry, my previous mail bounced back, as it was over 50 KB. <br><br>I changed the ffG43a1 to include the GTP and GDP which I got from a previous post here. {<a href="http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html</a>}<br><br>I changed some structure like giving comment with ; as the origicanal # was giving error. but now it tells me there is an error that 05* is not found in the atom type database.<br>
<br><br>Program pdb2gmx, VERSION 3.3.1<br>Source code file: resall.c, line: 148<br><br>Fatal error:<br>Atom type O5* (residue GTP) not found in atomtype database<br>-------------------------------------------------------<br><br><br><br>I am including the file here .the GTP residue is at the bottom of the file.<br><br>
         <a href="https://netfiles.uiuc.edu/tezaz2/shared/ffG43a1.rtp" target="_NEW">https://netfiles.uiuc.edu/tezaz2/shared/ffG43a1.rtp</a><br><br>Is there any other GTP and GDP residue for the force field 43a1?<br><br>Thanks in advance.<br><br>Tawhid<br><br><br><br><br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">----- Original Message ----<br>From: Justin A. Lemkul <jalemkul@vt.edu><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Monday, November 26, 2007 9:14:37 PM<br>Subject: Re: [gmx-users] pdb2gmx error<br><br>Quoting Tawhid Ezaz <<a ymailto="mailto:ezaztaw@yahoo.com" href="mailto:ezaztaw@yahoo.com">ezaztaw@yahoo.com</a>>:<br><br>> Thanks a lot Justin. It worked really nice.<br>><br>> now I am stuck with another problem. I need to add the Building block
GTP and<br>> GDP in 43a1, as I need to get the topology of a tubulin monomer. I
got the<br>> file from a old post here.<br>><br>> <a href="http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html</a><br>><br>> I copied and pasted it into my file, yet, as the structure doesn't
match it<br>> gave several errors.<br>><br>> is there any way to fix this?<br><br>That depends entirely upon what your errors are and what you're trying
to do. <br>Please provide more details.<br><br>-Justin<br><br>><br>> Thanks a lot for your help.<br>><br>> Tawhid<br>><br>><br>><br>> ----- Original Message ----<br>> From: Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> To: Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> Sent: Monday, November 26, 2007 7:14:43 PM<br>> Subject: Re: [gmx-users] pdb2gmx error<br>><br>><br>> Quoting Tawhid Ezaz <<a ymailto="mailto:ezaztaw@yahoo.com" href="mailto:ezaztaw@yahoo.com">ezaztaw@yahoo.com</a>>:<br>><br>> > Hi,<br>> ><br>> > I have just started to learn gromacs. I am facing a problem to make<br>> topology<br>> > file of a myoglobin. I got the pdb file from the csc tutorial.<br>> ><br>> > When i am
running the pdb2gmx with<br>> ><br>> > pdb2gmx -f conf.pdb -p topol.top<br>> ><br>> > i get the message, HEME148 CAB1428 0.569<br>> > HEME148 CAC1437 0.562 0.820<br>> > N-terminus: NH3+<br>> > C-terminus: COO-<br>> > Now there are 148 residues with 1451 atoms<br>> > -------------------------------------------------------<br>> > Program pdb2gmx, VERSION 3.3.1<br>> > Source code file: pdb2top.c, line: 570<br>> ><br>> > Fatal error:<br>> > atom N not found in residue 1ACE while combining tdb and rtp<br>> > -------------------------------------------------------<br>> ><br>> > I was using 43a1 force field (0), {but none of them works}.<br>> ><br>> > i read some previous post and got the idea that there should be a N<br>> atom with<br>> > should be linked with ACE, but my conf.pdb files does not have any.
I<br>> have<br>> > topol.top file from the tutorial but didn't show how I can generate<br>> that.<br>><br>> Use the -ter option with pdb2gmx, and select 'none' when prompted.<br>> That way,<br>> pdb2gmx does not look for an N-terminal nitrogen (which is obviously<br>> absent in<br>> an acetyl group).<br>><br>> -Justin<br>><br>> ><br>> > I am a totally newbie, thus I am wondering what should I do. Which<br>> file I<br>> > should correct to get rid of those? Do I need to know the bonding
of<br>> every<br>> > atom in the molecule for that?<br>> ><br>> > Thanks in advance<br>> ><br>> > Tawhid<br>> ><br>> ><br>> ><br>> ><br>> ><br>><br>><br>><br>> ========================================<br>><br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> <a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@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 ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a
href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.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<br>> posting!<br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" 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>><br>><br>><br>><br><br><br><br>========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br><a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@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 ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.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
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