Dear Justin,<br><br>1- Unfortunately, I am having difficulty running the simple program pdb2gmx with pdb file you sent me for Hexane.. I have in working directory pdb file and rtp files: <br>Hexane-PRODRG.pdb rtp.pdb<br> <br>
pdb2gmx -f Hexane-PRODRG.pdb -o Hexane.gro -p Hexane.top >& output.pdb2gmx<br><br>output.pdb2gmx says:<br><br>Opening library file /chem_soft/gromacs/share/gromacs/top/FF.dat<br><br>2-can you please tell me why I need rtp file? previously I just created pdb file and used x2top an dI had no rtp file...<br>
<br>Thank you for your help.<br><br>******************************************************************<br>Hexane-PRODRG.pdb:<br><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>*******************************rtp.pdb :<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> C5 H52<br> C5 C6<br> C6 H61<br> C6 H62<br> C6 H63<br><br><br><br>****************************************************************************************Also I have tried x2top comamnd: x2top -f Hexane-PRODRG.pdb -o Hexane.top -alldih -ff oplsaa -name HEX <br>
as you suggested I am using -alldih flag to generate all dihedrals<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f Hexane-PRODRG.pdb Input Structure file: gro g96 pdb tpr tpb tpa<br>
-o Hexane.top Output, Opt! Topology file<br> -r out.rtp Output, Opt. Residue Type file used by pdb2gmx<br><br>Option Type Value Description<br>------------------------------------------------------<br>
-[no]h bool no Print help info and quit<br>-nice int 0 Set the nicelevel<br>-ff string oplsaa Force field for your simulation. Type "select"<br> for interactive selcection.<br>
-[no]v bool no Generate verbose output in the top file.<br>-nexcl int 3 Number of exclusions<br>-[no]H14 bool yes Use 3rd neighbour interactions for hydrogen atoms<br>-[no]alldih bool yes Generate all proper dihedrals<br>
-[no]remdih bool no Remove dihedrals on the same bond as an improper<br>-[no]pairs bool yes Output 1-4 interactions (pairs) in topology file<br>-name string HEX Name of your molecule<br>-[no]pbc bool yes Use periodic boundary conditions.<br>
-[no]pdbq bool no Use the B-factor supplied in a pdb file for the<br> atomic charges<br>-[no]param bool yes Print parameters in the output<br>-[no]round bool yes Round off measured values<br>
-kb real 400000 Bonded force constant (kJ/mol/nm^2)<br>-kt real 400 Angle force constant (kJ/mol/rad^2)<br>-kp real 5 Dihedral angle force constant (kJ/mol/rad^2)<br><br>Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat<br>
WARNING: masses will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>Opening library file /chem_soft/gromacs/share/gromacs/top/atommass.dat<br>Entries in atommass.dat: 178<br>
WARNING: vdwradii will be determined based on residue and atom names,<br> this can deviate from the real mass of the atom type<br>Opening library file /chem_soft/gromacs/share/gromacs/top/vdwradii.dat<br>Entries in vdwradii.dat: 28<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/dgsolv.dat<br>Entries in dgsolv.dat: 7<br>Opening library file /chem_soft/gromacs/share/gromacs/top/electroneg.dat<br>Entries in electroneg.dat: 71<br>Opening library file /chem_soft/gromacs/share/gromacs/top/elements.dat<br>
Entries in elements.dat: 218<br>Looking whether force field files exist<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.rtp<br>Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.n2t<br>
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.n2t<br>There are 23 name to type translations<br>Generating bonds from distances...<br>atom 0<br><br><br>