<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>Hi,<br>I want to know, by default g_rms calculates RMSD on which atoms set - backbone, all atoms or c-alphas ? How do i modify these settings ?<br><br>Regards,<br>Nikhil<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><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> Mark Abraham <Mark.Abraham@anu.edu.au><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> Monday, 20 July, 2009 7:35:29 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] H-Db error<br></font><br>nikhil damle
wrote:<br>> 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>> <br>> <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><br>That looks weird. Try spaces, not tabs. What does "pdb2gmx -debug -yourflags" say? If you have an empty line at the end, try removing it.<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><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
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