Hello,<br><br>I am trying to generate gro and top file with pdb2gmx program. I have made a copy of ffoplsaa.rtp from library to working directory and added Hexane molecule residue to the beginning of the ffoplsaa.rtp.<br><br>
<br>*****************************************.<br>.<br>.<br>.<br>.<br>.<br>; Col 4: Type of improper dihedrals<br>; Col 5: Generate all dihedrals if 1, only heavy atoms of 0.<br>; Col 6: Number of excluded neighbors for nonbonded interactions<br>
; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1<br>; Col 8: Remove propers over the same bond as an improper if it is 1<br>; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih<br> 1 1 3 1 1 3 1 0<br>
<br>[ HEX ]<br> [ atoms ]<br> C1 opls_157 -0.180 1<br> H11 opls_140 0.060 1<br> H12 opls_140 0.060 1<br> H13 opls_140 0.060 1<br> C2 opls_158 -0.120 2<br> H21 opls_140 0.060 2<br>
H22 opls_140 0.060 2<br> C3 opls_158 0.120 3<br> H31 opls_140 0.060 3<br> H32 opls_140 0.060 3<br> C4 opls_158 -0.120 4<br> H41 opls_140 0.060 4<br>
H42 opls_140 0.060 4<br> C5 opls_158 -0.120 5<br> H51 opls_140 0.060 5<br> H52 opls_140 0.060 5<br> C6 opls_157 -0.180 6<br> H61 opls_140 0.060 6<br>
H62 opls_140 0.060 6<br> H63 opls_140 0.060 6<br> [ bonds ]<br> C1 H11<br> C1 H12<br> C1 H13<br> C1 C2<br> C2 H21<br> C2 H22<br> C2 C3<br> C3 H31<br> C3 H32<br>
C3 C4<br> C4 H41<br> C4 H42<br> C4 C5<br> C5 H51<br><br>[ ACE ]<br> [ atoms ]<br> CH3 opls_135 -0.180 1<br> HH31 opls_140 0.060 1<br> HH32 opls_140 0.060 1<br> HH33 opls_140 0.060 1<br>
C opls_235 0.500 2<br> O opls_236 -0.500 2<br> [ bonds ]<br> CH3 HH31<br> CH3 HH32<br> CH3 HH33<br> CH3 C<br> C O<br>[ impropers ]<br> CH3 +N C O improper_O_C_X_Y<br>
<br>[ ALA ]<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_135 -0.180 2<br> HB1 opls_140 0.060 2<br>
HB2 opls_140 0.060 2<br>.<br>.<br>.<br>.<br>.<br><br>***********************************************************************************commans I type in:<br><br><br>pdb2gmx -f Hexane-PRODRG.pdb -o Hexane-PRODRG.gro -p Hexane-PRODRG.top -ff oplsaa >& output.pdb2gmx<br>
<br>I do not get gro file at all and top file I get contains the following comments only!:<br><br>;********************************************************************<br>; File 'Hexane-PRODRG.top' was generated<br>
; By user: moeed (500)<br>; On host: moeed-desktop<br>; At date: Sun May 9 10:47:26 2010<br>;<br>; This is your topology file<br>; "This Doesn't Suck, It's a Black Hole !" (K.A. Feenstra)<br>
;<br>; Include forcefield parameters<br>#include "ffoplsaa.itp"<br><br><br><br>***************************************<br><br><br><br><br><br><br>***************Hexane-PRODRG.pdb<br><br>CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1<br>
ATOM 1 C1 HEX 1 8.330 1.510 -0.010 0.00 0.00 C<br>ATOM 2 H11 HEX 1 9.281 1.200 -0.024 0.00 0.00 H<br>ATOM 3 H12 HEX 1 8.154 2.080 -0.813 0.00 0.00 H<br>
ATOM 4 H13 HEX 1 8.166 2.044 0.820 0.00 0.00 H<br>ATOM 5 C2 HEX 1 7.400 0.300 -0.030 0.00 0.00 C<br>ATOM 6 H21 HEX 1 7.584 -0.267 0.773 0.00 0.00 H<br>
ATOM 7 H22 HEX 1 7.573 -0.231 -0.860 0.00 0.00 H<br>ATOM 8 C3 HEX 1 5.940 0.730 -0.010 0.00 0.00 C<br>ATOM 9 H31 HEX 1 5.754 1.291 -0.816 0.00 0.00 H<br>
ATOM 10 H32 HEX 1 5.769 1.266 0.817 0.00 0.00 H<br>ATOM 11 C4 HEX 1 5.010 -0.480 -0.020 0.00 0.00 C<br>ATOM 12 H41 HEX 1 5.192 -1.038 0.790 0.00 0.00 H<br>
ATOM 13 H42 HEX 1 5.186 -1.020 -0.843 0.00 0.00 H<br>ATOM 14 C5 HEX 1 3.540 -0.050 -0.010 0.00 0.00 C<br>ATOM 15 H51 HEX 1 3.357 0.507 -0.820 0.00 0.00 H<br>
ATOM 16 H52 HEX 1 3.363 0.489 0.813 0.00 0.00 H<br>ATOM 17 C6 HEX 1 2.610 -1.270 -0.020 0.00 0.00 C<br>ATOM 18 H61 HEX 1 1.658 -0.964 -0.013 0.00 0.00 H<br>
ATOM 19 H62 HEX 1 2.780 -1.812 -0.843 0.00 0.00 H<br>ATOM 20 H63 HEX 1 2.785 -1.830 0.790 0.00 0.00 H<br>END<br>************************************************************************************************<br>