 Question about Urea parameters (Caflisch and Karplus, 1995)
|
Joined: Oct 2006
Posts: 1
Forum Member
|
OP
Forum Member
Joined: Oct 2006
Posts: 1 |
I took the parameters that Amedeo Caflisch posted to these boards (from his 1995 paper with Karplus) and pasted them into the top_all27_prot_lipid_na file (the exact format is pasted below). I've tried using this file to generate a psf from a pdb file containing urea. However the program (psfgen from the VMD package) doesn't seem able to build urea.
I'm wondering if this is because the parameters will only work with charmm22 or if I haven't added them to the topology file correctly.
Anyone have any suggestions? The information in the topology file is:
============================================================ RESI UREA 0.00 ! urea by A. Caflisch December 19, 1995 GROUP ATOM O O -0.51 ATOM C C 0.51 GROUP ATOM N1 NH2 -0.62 ATOM H11 H 0.31 ATOM H12 H 0.31 GROUP ATOM N2 NH2 -0.62 ATOM H21 H 0.31 ATOM H22 H 0.31 BOND O C C N1 C N2 N1 H11 N1 H12 BOND N2 H21 N2 H22 IMPH C O N1 N2 IMPH N1 C H11 H12 IMPH N2 C H21 H22 PATCHING FIRS NONE LAST NONE
============================================================
Thanks.
Last edited by patwin2; 10/13/06 05:08 PM.
|
|
|
 Re: Question about Urea parameters (Caflisch and Karplus, 1995)
|
Joined: Jul 2004
Posts: 53
Forum Member
|
Forum Member
Joined: Jul 2004
Posts: 53 |
I think the dihedrals are missing. I will see to it as I need a molecule of urea as well.
best regard, zee
PS: I hope it's not to late.
|
|
|
 Re: Question about Urea parameters (Caflisch and Karplus, 1995)
|
Joined: Sep 2003
Posts: 4,803 Likes: 2
Forum Member
|
Forum Member
Joined: Sep 2003
Posts: 4,803 Likes: 2 |
DIHEdrals are not needed in the RTF. As to why psfgen cannot build urea I suggest asking the VMD/NAMD community. Our urea definition is posted below (compatible with top/par_all22_prot):
RTF: RESI UREA 0.0 ! Based on OPLS Urea. Jorgensen JACS(1993) 115 9271-9275 ! Caballe&Nilsson (2005). J. Mol. Struct. THEOCHEM 758:137-146. GROUP ATOM N1 NH2 -0.569 ! geometry from Swaminathan et al (1984) Acta ATOM H11 H 0.416 ! Cryst B40, 300 ATOM H12 H 0.333 ! NOTE: approximation to OPLS, using std ASN types ATOM C CC 0.142 ! and charges to agree w/ results of Karlstrom et al ATOM O O -0.502 ATOM N2 NH2 -0.569 ATOM H21 H 0.333 ATOM H22 H 0.416 BOND N1 H11 N1 H12 N1 C BOND C O C N2 N2 H21 N2 H22 ! IMPROPER SETUP TAKEN FROM ASN&GLN IMPR C N2 N1 O IMPR N1 C H11 H12 IMPR N2 C H21 H22
ACCE O C DONOR H11 N1 DONOR H12 N1 DONOR H21 N2 DONOR H22 N2 IC H11 N1 C N2 1.0 119.0 180.0 117.0 1.35 IC H11 C *N1 H12 1.0 119.0 180.0 120.0 1.0 IC O N2 *C N1 1.26 121.0 180.0 117.0 1.35 IC H22 N2 C N1 1.0 119.0 180.0 117.0 1.35 IC H22 C *N2 H21 1.0 119.0 180.0 120.0 1.0 PATCHING FIRS NONE LAST NONE
parameter file: ANGLES NH2 CC NH2 130.0 117.0 ! For urea. LNI Sept 1998, analog w/ ! NR2 CPH2 NR1, geometry from Acta CrystB40 p300
DIHEDRALS H NH2 CC NH2 1.4 2 180.0 ! For urea. LNI sept 1998 ! analogy with entry for acetamide H NH2 CC CT2 IMPROPER O NH2 NH2 CC 45.0000 0 0.0000 ! For urea. LNI sept 1998 ! analogy with entry for acetamide O HA NH2 CC
Lennart Nilsson Karolinska Institutet Stockholm, Sweden
|
|
|
 Re: Question about Urea parameters (Caflisch and Karplus, 1995)
|
Joined: Jul 2004
Posts: 113
Forum Member
|
Forum Member
Joined: Jul 2004
Posts: 113 |
Dear Lennart,
I ran two simulations (urea in a water box) with two different force fields for urea (Caflisch's and yours that I found in this forum), and calculated the interaction energy between urea and water using the VMD tool. Here is what I have:
Caflisch's : ~ -30 kcal/mol yours : ~ -50 kcal/mol
The size of water box is 20 x 20 x 20, and I ran 1 ns for each force field. The difference is huge. I wonder which one is close to an experimental value. Could you give some comments on it ? Thank you.
|
|
|
 Re: Question about Urea parameters (Caflisch and Karplus, 1995)
|
Joined: Dec 2005
Posts: 1,535
Forum Member
|
Forum Member
Joined: Dec 2005
Posts: 1,535 |
AFAIK, VMD does not have a force field engine. It is not clear from your post which software you used for simulating the system and calculating energies, what type of simulation you did and what kind of analysis was performed to obtain the values you're citing, leave alone what the meaning of these values is.
|
|
|
 Re: Question about Urea parameters (Caflisch and Karplus, 1995)
|
Joined: Jul 2004
Posts: 113
Forum Member
|
Forum Member
Joined: Jul 2004
Posts: 113 |
Sorry for confusion. I used NAMD for my simulations. I read in dcd file on VMD and used NAMD energy protocol to calculate the interaction energy between urea and water molecules (I have only one urea in my TIP3P water box).
Thanks.
|
|
|
 Re: Question about Urea parameters (Caflisch and Karplus, 1995)
|
Joined: Sep 2003
Posts: 4,803 Likes: 2
Forum Member
|
Forum Member
Joined: Sep 2003
Posts: 4,803 Likes: 2 |
This would be related to the enthalpic component of the free energy of transfer from gas-phase to aqueous solution, and I don't know if there is an experimental number available for this. The charges are not all that different between the two models though.
It would be interesting to know if you also find differences in the g(r) for water oxygens around the urea oxygen and nitrogens, and in urea translational and rotational diffusion. You may need more than 1 ns, but this is only a question of about an hour/ns of simulation in CHARMM, a little longer probably with NAMD but still manageable.
Lennart Nilsson Karolinska Institutet Stockholm, Sweden
|
|
|
 Re: Question about Urea parameters (Caflisch and Karplus, 1995)
|
Joined: Jul 2004
Posts: 113
Forum Member
|
Forum Member
Joined: Jul 2004
Posts: 113 |
Thank you for your comments. I'll look into g(r) and the diffusion. I wonder whether there is any references for comparison between two force fields.
|
|
|
 Re: Question about Urea parameters (Caflisch and Karplus, 1995)
|
Joined: Sep 2003
Posts: 8,524 Likes: 2
Forum Member
|
Forum Member
Joined: Sep 2003
Posts: 8,524 Likes: 2 |
There are several papers which compare protein force fields, which should be easy to find.
While perhaps not so easy to find*, there ought to be some experiment data for urea available, such as crystal and NMR studies, and maybe transfer free energy or free energy of solvation. In part because of the TIP3P water model, diffusion can be a bit tricky to compare between simulation and experiment. (We have a fairly detailed paper on this in press at JPC B.)
* The common use of urea as a denaturant tends to confound simple search strategies.
About the charges-- they look somewhat different to me, both in magnitude and symmetry assumptions (non-equivalent proton charges). The C=O dipole is also substantially changed.
Rick Venable computational chemist
|
|
|
 Re: Question about Urea parameters (Caflisch and Karplus, 1995)
|
Joined: Sep 2003
Posts: 4,803 Likes: 2
Forum Member
|
Forum Member
Joined: Sep 2003
Posts: 4,803 Likes: 2 |
Yes, the carbon charge is quite different. I hope our old papers on diffusion of TIP3P and comparison with experiment don't come out to badly - if I remember correctly motions in TIP3P are roughly twice as fast as experimentally observed, so it should, to first order, be a relatively straightforward correction. I look forward to reading your paper for more details!
Lennart Nilsson Karolinska Institutet Stockholm, Sweden
|
|
|
|
|