Hello all,<br><br> I have built a parameter file for the AOT surfactant molecule and tried to minimize the energy of a mixture of several of this molecule and water molecules but I have the warnings at the bottom part of this mail. Gromacs basically goes through all the lines of parameters starting from [ bonds ] and says the parameters are too few. I am also using the charmm force field. <br>
<br> Here is the way I constructed the aot.itp parameter file. I am not sure this is correct. Excerpts of the parameter file are belowl.<br><br>- I drew the AOT molecule and did the bond and angle connections in the molecule.The atom names are provided by the ffcharmm27.atp file. All values are obtained from the ffcharmmbon.itp file and ffcharmmnb.itp file. <br>
- I am not sure how to build the dihedrals since the are X's in the [ dihedrals ] section of the ffcharmmbon.itp file.<br><br>My question is: Why does the program say I have few parameters while I just out together parameters from the charmm27 force field? Please, if I am doing something wrong, can someone let me know? <br>
[ bonds ]<br>; i j func b0 kb<br>SL O2L 1 0.1448 451872.0<br>SL CTL1 1 0.1800 376560.0<br>CTL1 HAL1 1 0.1111 258571.2<br>[ angles ]<br>; i j k func th0 cth ub0 cub<br>
02L SL O2L 5 109.47 1087.84 0.245 29288.0<br>O2L SL CTL1 5 98.0 711.28 0.0 0.0<br>SL CTL1 HAL1 5 110.10 288.696 0.2179 18853.104<br>[ dihedrals ]<br>
; i j k l func phi0 cp mult<br>HAL1 CTL1 SL O2L 9 0.00 0.0 3<br>CTL2 OSL SL O2L 9 0.00 0.0 3<br>CL CTL1 SL O2L 9 0.00 0.0 3<br>X CTL1 CTL2 X 9 0.00 0.8368 3<br>
X CTL1 CTL2 X 9 0.00 0.8368 3<br>[ atoms ]<br>;name at.num mass charge ptype sigma epsilon<br>CL 6 12.01100 0.62 A 0.356359487256 0.29288 <br>HAL1 1 1.008000 0.09 A 0.235197261589 0.092048 <br>
HAL2 1 1.008000 0.09 A 0.238760856462 0.117152 <br>[ pairs ]<br>; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS<br>CTL1 CTL1 1 0.338541512893 0.04184<br>CTL1 CTL2 1 0.338541512893 0.04184<br>
CTL1 CTL3 1 0.338541512893 0.04184<br><br>WARNING 141 [file aot_2.itp, line 228]:<br> Too few parameters on line (source file toppush.c, line 1248)<br><br><br>WARNING 142 [file aot_2.itp, line 229]:<br> Too few parameters on line (source file toppush.c, line 1248)<br>
<br>Excluding 3 bonded neighbours molecule type 'AOT'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br><br>NOTE 1 [file aotwater.top, line 19]:<br> System has non-zero total charge: -1.350000e+01<br>
<br>processing coordinates...<br>double-checking input for internal consistency...<br>renumbering atomtypes...<br>converting bonded parameters...<br>initialising group options...<br>processing index file...<br>Analysing residue names:<br>
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>There are: 60 OTHER residues<br>There are: 0 PROTEIN residues<br>There are: 0 DNA residues<br>Analysing Other...<br>Making dummy/rest group for T-Coupling containing 1110 elements<br>
Making dummy/rest group for Acceleration containing 1110 elements<br>Making dummy/rest group for Freeze containing 1110 elements<br>Making dummy/rest group for Energy Mon. containing 1110 elements<br>Making dummy/rest group for VCM containing 1110 elements<br>
Number of degrees of freedom in T-Coupling group rest is 3192.00<br>Making dummy/rest group for User1 containing 1110 elements<br>Making dummy/rest group for User2 containing 1110 elements<br>Making dummy/rest group for XTC containing 1110 elements<br>
Making dummy/rest group for Or. Res. Fit containing 1110 elements<br>Making dummy/rest group for QMMM containing 1110 elements<br>T-Coupling has 1 element(s): rest<br>Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>
Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>VCM has 1 element(s): rest<br>XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>
QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br><br>NOTE 2 [file aotwater_min.mdp, line unknown]:<br> You are using a plain Coulomb cut-off, which might produce artifacts.<br>
You might want to consider using PME electrostatics.<br><br><br>This run will generate roughly 1 Mb of data<br>writing run input file...<br><br>There were 2 notes<br><br>There were 142 warnings<br><br>-------------------------------------------------------<br>
Program grompp, VERSION 4.0.5<br>Source code file: gmx_fatal.c, line: 481<br><br>Fatal error:<br>Too many warnings (142), grompp terminated.<br>If you are sure all warnings are harmless, use the -maxwarn option.<br>-------------------------------------------------------<br>
<br><br>I appreciate your answers.<br><br>Lum<br>