Hi, XAvier,<br><br>Sorry for that mistake. Yes, exactly PRODRG is not giving the non-polar hydrogens. There I am using the GROMOS96.1 FF. So is there any way to get the proper .itp file? I mean any other online server like PRODRG? Or How can I derive the proper .itp file manually?<br>
Any suggestion is welcome. Thanks a lot for the prompt reply.<br><br>Regards,<br><br>Anirban<br><br><div class="gmail_quote">On Wed, Apr 14, 2010 at 3:25 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
You are missing HB1 and HB2, not HB2 and HB3 :))<br>
<br>
This is due to the force field our are using. Gromos I presume: it<br>
uses the united H idea: non-polar H are not explicitly modeled.<br>
<br>
you should be able to erase those from your gro file, but I would<br>
suggest you get into some literature about the FF you use.<br>
<br>
XAvier.<div><div></div><div class="h5"><br>
<br>
On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote:<br>
<br>
</div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
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></div></div>
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