Hi ALL,<br><br>I have a ligand LDOPA with 25 atoms (including all hydrogens).:<br>-------------------------------------------------------------------------------------------------------------------------------------------<br>
DAH COORDS<br> 25<br> 1DAH O 1 5.988 5.216 9.128<br> 1DAH C 2 5.980 5.110 9.194<br> 1DAH OXT 3 5.951 4.985 9.139<br> 1DAH CA 4 6.001 5.107 9.349<br> 1DAH HA 5 5.935 5.027 9.384<br>
1DAH N 6 6.140 5.064 9.387<br> 1DAH H2 7 6.161 4.977 9.343<br> 1DAH H3 8 6.137 5.056 9.486<br> 1DAH H1 9 6.206 5.133 9.356<br> 1DAH CB 10 5.952 5.236 9.422<br>
1DAH HB1 11 5.985 5.320 9.362<br> 1DAH HB2 12 5.999 5.231 9.520<br> 1DAH CG 13 5.802 5.258 9.450<br> 1DAH CD2 14 5.761 5.333 9.565<br> 1DAH HD2 15 5.836 5.375 9.632<br>
1DAH CE2 16 5.623 5.353 9.592<br> 1DAH OE2 17 5.589 5.425 9.704<br> 1DAH HE2 18 5.672 5.454 9.752<br> 1DAH CZ 19 5.523 5.297 9.503<br> 1DAH OZ 20 5.387 5.314 9.525<br>
1DAH HZ 21 5.335 5.268 9.453<br> 1DAH CE1 22 5.564 5.223 9.389<br> 1DAH HE1 23 5.489 5.181 9.321<br> 1DAH CD1 24 5.701 5.203 9.362<br> 1DAH HD1 25 5.731 5.146 9.274<br>
1.02033 1.02033 1.02033<br>--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br><br> I derived the topology file from PRODRG server. However the .itp file is giving only 22 atoms definition and 3 of the hydrogen atoms are missing:<br>
<br>---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>DAH 3<br><br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br>
1 OM 1 DAH O 1 -0.715 15.9994 <br> 2 C 1 DAH C 1 0.387 12.0110 <br> 3 OM 1 DAH OXT 1 -0.716 15.9994 <br> 4 CH1 1 DAH CA 1 0.178 13.0190 <br>
5 NL 1 DAH N 1 0.683 14.0067 <br> 6 H 1 DAH H2 1 0.010 1.0080 <br> 7 H 1 DAH H3 1 0.010 1.0080 <br> 8 H 1 DAH H1 1 0.011 1.0080 <br>
9 CH2 1 DAH CB 1 0.152 14.0270 <br> 10 C 1 DAH CG 2 -0.020 12.0110 <br> 11 CR1 1 DAH CD2 2 0.001 12.0110 <br> 12 HC 1 DAH HD2 2 0.019 1.0080 <br>
13 C 1 DAH CE2 3 0.130 12.0110 <br> 14 OA 1 DAH OE2 3 -0.197 15.9994 <br> 15 H 1 DAH HE2 3 0.051 1.0080 <br> 16 C 1 DAH CZ 3 0.130 12.0110 <br>
17 OA 1 DAH OZ 3 -0.197 15.9994 <br> 18 H 1 DAH HZ 3 0.051 1.0080 <br> 19 CR1 1 DAH CE1 3 0.001 12.0110 <br> 20 HC 1 DAH HE1 3 0.031 1.0080 <br>
21 CR1 1 DAH CD1 4 0.000 12.0110 <br> 22 HC 1 DAH HD1 4 0.000 1.0080 <br><br>[ bonds ]<br>----------------------------------------------------------------------------------------------------------------------------------------------------------------<br>
So you can see that HA, HB2 and HB3 hydrogens are missing here. So I am getting error messages popped by grompp commands. How can I get the definition of those missing 3 H atoms? Is it ok if I delete those 3 H atoms from my .gro file and proceed? If not then how to derive parameters for them? Any suggestion is welcome.<br>
Thanks a lot in advance.<br><br>Regards,<br><br>Anirban<br>