<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear Sir,<br> <br><br> I want to simulate a protein with a CA2+ ion and one crystal water using G431 force field, simulation of the protein without the metal ion went off successfully,But while running the simulation with the metal ion it's giving a fatal error during position restrained molecular dynamics, <br><br>"Fatal error:<br>Group CA2+ not found in indexfile.<br>Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.<br>In that case use the '-n' option.<br>"<br>Upto energy minimisation I have modified aminoacids.dat and other required files, & it's not giving any error messege. During PR dynamics it's giving an error messege <br>"-------------------------------------------------------<br>Program grompp, VERSION 4.0.5<br>Source code file: readir.c, line:
1075<br><br>Fatal error:<br>1 atoms are not part of any of the T-Coupling groups<br>-------------------------------------------------------<br>"<br> If I incorporate CA2+ ion in the mdp file it's giving "Fatal error:<br>Group CA2+ not found in indexfile.<br>Maybe you have non-default goups in your mdp file, while not using the '-n' option of grompp.<br>In that case use the '-n' option.<br>"<br>if I use -n option it's giving<br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.5<br>Source code file: futil.c, line: 330<br><br>File input/output error:<br>index.ndx<br>-------------------------------------------------------<br>I don't understand what else files should be considered and manually edited.Please help.While running pdb2gmx CA2+ ion is considered as follows.<br><br>type resnr residue<br>CA2+ CA CA<br><br>Please suggest what should be taken
into account while running the simulation with the metal ion.<br><br><br>regards<br><span style="font-style: italic; font-family: symbol;">Sangeeta Kundu</span><br></td></tr></table><br>
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