Anirban Ghosh wrote:
Hi XAvier,
Thanks for the reply. Actually I want to use this ligand with a protein
and run the complex using ffG43a2 force-field of GROMACS4.0.7. So is it
correct to leave away those 3 hydrogens HA, HB1 and HB2, which are not
explicitly described? Because in protein-ligand complexes, hydrogen bond
formations between the ligand and the protein are important? So should I
continue with this .itp file with 3 less hydrogens?
Thanks again.
Consider basic biochemistry - do hydrogen bonds involving C-H bonds usually
form? I would strongly recommend reading the primary literature for the
GROMOS96 force fields, as well as any other material regarding united-atom force
fields you can find. It sounds like you need a bit more fundamental
understanding of what's going on.
Besides, I wouldn't use that topology anyway. As I continually advise on this
list, a PRODRG output is more often than not (read: basically always!) incorrect
in some fashion. L-DOPA should be derived from tyrosine, therefore it is a
reasonable assumption to think that its parameters should somewhat resemble this
amino acid. Look at the topology - each of your C-H bonds in the aromatic ring
has different charges, which certainly is not right! You should at least have
functional group consistency.
Before you waste your time doing a simulation with bogus parameters, you will
have to consider parameterization (an advanced topic, indeed):
http://www.gromacs.org/Documentation/How-tos/Parameterization
In general, functional groups within GROMOS96 are very transferrable between
different molecules (from personal experience), but you still have to
demonstrate that your system is sound to reviewers. I know if I ever got a
paper that just said "we used PRODRG" I would immediately want to see the
parameters and know the justification for using them.
-Justin
Regards,
Anirban
On Wed, Apr 14, 2010 at 3:50 PM, XAvier Periole <[email protected]
<mailto:[email protected]>> wrote:
You have the proper itp file for the GROMOS FF. Some H are not
explicitly
described!
On Apr 14, 2010, at 12:05 PM, Anirban Ghosh wrote:
Hi, XAvier,
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?
Any suggestion is welcome. Thanks a lot for the prompt reply.
Regards,
Anirban
On Wed, Apr 14, 2010 at 3:25 PM, XAvier Periole <[email protected]
<mailto:[email protected]>> wrote:
You are missing HB1 and HB2, not HB2 and HB3 :))
This is due to the force field our are using. Gromos I presume: it
uses the united H idea: non-polar H are not explicitly modeled.
you should be able to erase those from your gro file, but I would
suggest you get into some literature about the FF you use.
XAvier.
On Apr 14, 2010, at 11:36 AM, Anirban Ghosh wrote:
Hi ALL,
I have a ligand LDOPA with 25 atoms (including all
hydrogens).:
-------------------------------------------------------------------------------------------------------------------------------------------
DAH COORDS
25
1DAH O 1 5.988 5.216 9.128
1DAH C 2 5.980 5.110 9.194
1DAH OXT 3 5.951 4.985 9.139
1DAH CA 4 6.001 5.107 9.349
1DAH HA 5 5.935 5.027 9.384
1DAH N 6 6.140 5.064 9.387
1DAH H2 7 6.161 4.977 9.343
1DAH H3 8 6.137 5.056 9.486
1DAH H1 9 6.206 5.133 9.356
1DAH CB 10 5.952 5.236 9.422
1DAH HB1 11 5.985 5.320 9.362
1DAH HB2 12 5.999 5.231 9.520
1DAH CG 13 5.802 5.258 9.450
1DAH CD2 14 5.761 5.333 9.565
1DAH HD2 15 5.836 5.375 9.632
1DAH CE2 16 5.623 5.353 9.592
1DAH OE2 17 5.589 5.425 9.704
1DAH HE2 18 5.672 5.454 9.752
1DAH CZ 19 5.523 5.297 9.503
1DAH OZ 20 5.387 5.314 9.525
1DAH HZ 21 5.335 5.268 9.453
1DAH CE1 22 5.564 5.223 9.389
1DAH HE1 23 5.489 5.181 9.321
1DAH CD1 24 5.701 5.203 9.362
1DAH HD1 25 5.731 5.146 9.274
1.02033 1.02033 1.02033
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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:
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
DAH 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 DAH O 1 -0.715 15.9994
2 C 1 DAH C 1 0.387 12.0110
3 OM 1 DAH OXT 1 -0.716 15.9994
4 CH1 1 DAH CA 1 0.178 13.0190
5 NL 1 DAH N 1 0.683 14.0067
6 H 1 DAH H2 1 0.010 1.0080
7 H 1 DAH H3 1 0.010 1.0080
8 H 1 DAH H1 1 0.011 1.0080
9 CH2 1 DAH CB 1 0.152 14.0270
10 C 1 DAH CG 2 -0.020 12.0110
11 CR1 1 DAH CD2 2 0.001 12.0110
12 HC 1 DAH HD2 2 0.019 1.0080
13 C 1 DAH CE2 3 0.130 12.0110
14 OA 1 DAH OE2 3 -0.197 15.9994
15 H 1 DAH HE2 3 0.051 1.0080
16 C 1 DAH CZ 3 0.130 12.0110
17 OA 1 DAH OZ 3 -0.197 15.9994
18 H 1 DAH HZ 3 0.051 1.0080
19 CR1 1 DAH CE1 3 0.001 12.0110
20 HC 1 DAH HE1 3 0.031 1.0080
21 CR1 1 DAH CD1 4 0.000 12.0110
22 HC 1 DAH HD1 4 0.000 1.0080
[ bonds ]
----------------------------------------------------------------------------------------------------------------------------------------------------------------
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.
Thanks a lot in advance.
Regards,
Anirban
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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