Hi,<br>I'm using the OPLS force field.<br><br>[ PHE ]<br> [ atoms ]<br> N opls_238 -0.500 1<br> H opls_241 0.300 1<br> CA opls_224B 0.140 1<br> HA opls_140 0.060 1<br>
CB opls_149 -0.005 2<br> HB1 opls_140 0.060 2<br> HB2 opls_140 0.060 2<br> CG opls_145 -0.115 2<br> CD1 opls_145 -0.115 3<br> HD1 opls_146 0.115 3<br>
CD2 opls_145 -0.115 4<br> HD2 opls_146 0.115 4<br> CE1 opls_145 -0.115 5<br> HE1 opls_146 0.115 5<br> CE2 opls_145 -0.115 6<br> HE2 opls_146 0.115 6 <br>
CZ opls_145 -0.115 7 <br> HZ opls_146 0.115 7<br> C opls_235 0.500 8<br> O opls_236 -0.500 8<br><br>I want to attach "CL" atom instead of HZ<br>i made my pdb but when i use pdb2gmx, it adds HZ automatically in gro and top files.<br>
What should i do to get rid of this HZ and attach CL instead.<br>(I edited top and gro files and remove HZ from them, it seemed to work properly at first, but when i tried to do energy minimization, it had errors in top file<br>
and i realized that it couldn't recognized the bond between CL and CZ):<br><br>ERROR 1 [file topol.top, line 150]:<br> No default Bond types<br><br><br>ERROR 2 [file topol.top, line 422]:<br> No default Angle types<br>
<br><br>ERROR 3 [file topol.top, line 423]:<br> No default Angle types<br><br> <i>"topol.top":</i><br>...<br> 58 opls_146 3 PHE HE2 22 0.115 1.008 ; qtot 0.9<br> 59 opls_145 3 PHE CZ 23 -0.115 12.011 ; qtot 0.785<br>
60 opls_271 3 PHE C 24 0.7 12.011 ; qtot 1.6<br> 61 opls_272 3 PHE O1 24 -0.8 15.9994 ; qtot 0.8<br> 62 opls_272 3 PHE O2 24 -0.8 15.9994 ; qtot 0<br>
63 opls_135 4 EtOH CB 25 -0.18 12.011 ; qtot -0.18<br> 64 opls_140 4 EtOH HB1 25 0.06 1.008 ; qtot -0.12<br> 65 opls_140 4 EtOH HB2 25 0.06 1.008 ; qtot -0.06<br>
66 opls_401 5 CL CL 26 -1 35.453 ; qtot -1.06<br>...<br>[ bonds ]<br>...<br> 59 66 1 <br> 60 61 1 <br> 60 62 1 <br> 63 64 1 <br> 63 65 1 <br>
...<br>[ angles ]<br>...<br> 58 57 59 1 <br> 55 59 57 1 <br> 55 59 66 1 <br> 57 59 66 1 <br> 45 60 61 1 <br> 45 60 62 1 <br> 61 60 62 1 <br>
64 63 65 1 <br>...<br> <br>