<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>This is how i have modified the entry as i myself created the parameter file for phosphothreonine. This is normal NH hydrogen n no extra added=>directly copied from threonine. So y there is an error msg ? i added this residue in aminoacids.dat file as well. and 2ns line is tab separated. Is there any other formatting to b done ??<br><br><br>TPO 1<br>1 1 H N -C CA<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><br>This is error msg i get: (I also checked h_db.c programme but could not get much help abt the error
msg)<br>---------------------------------------------------------------<br>All occupancies are one<br>Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.atp<br>Atomtype 1<br>Reading residue database... (ffG43a1)<br>Opening library file /home/nikhil/softwares/GROMACS4..0.5/share/gromacs/top/ffG43a1.rtp<br>Residue 97<br>Sorting it all out...<br>Opening library file /home/nikhil/softwares/GROMACS4.0.5/share/gromacs/top/ffG43a1.hdb<br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.0.5<br>Source code file: h_db.c, line: 162<br><br>Fatal error:<br>Error reading from file ffG43a1<br>-------------------------------------------------------------------------------------------<br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul
<jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sunday, 19 July, 2009 5:14:35 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] H-Db error<br></font><br><br><br>nikhil damle wrote:<br>> Hello,<br>> Thanks for the reply. I am trying to add N-H hydrogen of a residue which is tab separated formate; just like other residues. if i remove this H from .hdb file, file can be read and pdb2gmx gives missing atom error. But when i have it in the file, it can not read it. if there were version related problem, it should give same error even after removing this H. i m using Gromacs-4.0.5 on linux machine. so no OS related problems possible<br>> <br><br>Did you properly increment the line indicating how many entries pdb2gmx should find in that section? For example, if I'm
playing around with Asn, and adding some H somewhere:<br><br>ASN 2<br><br>becomes<br><br>ASN 3<br><br>before pdb2gmx can properly handle the addition.<br><br>It would be helpful to see the exact error message.<br><br>-Justin<br><br>> Regards,<br>> Nikhil<br>> <br>> ------------------------------------------------------------------------<br>> *From:* Mark Abraham <<a ymailto="mailto:Mark.Abraham@anu..edu.au" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</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:* Sunday, 19 July, 2009 2:43:05 PM<br>> *Subject:* Re: [gmx-users] H-Db error<br>> <br>> nikhil damle wrote:<br>> > Hi,<br>> > I added peptide H to the the new residue i added to .rtp file in the ffG43a1.hdb file But the pdb2gmx gives
error saying it can not read hdb file. If i remove this H from .hdb file, it gives error of missing atom. How should i resolve this problem ? y can pdb2gmx not read hdb file if i add one extra H ??<br>> <br>> If your version of the .hdb file can't be read, then you've broken the format (see chapter 5), or created a file that does not adhere to the right conventions (e.g. by having Windows-style line endings - fix using dos2unix utility), or mangled the file permissions, or quite a few other possiblities.<br>> <br>> Mark<br>> _______________________________________________<br>> gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
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href="http://in.rd.yahoo.com/tagline_buzz_1/*http://in.buzz.yahoo.com/" target="_blank">http://in.rd.yahoo.com/tagline_buzz_1/*http://in.buzz.yahoo.com/</a>>.<br>> <br>> <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://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 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>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (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://lists.gromacs.org/mailman/listinfo/gmx-users"
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