khuchtumur wrote:
Hi Justin,
Thank you for writing this clarification. I'm still having a bit of a
problem with the anomeric -OH group giving LINCS warnings during
equilibration though.
I am trying to parametrize a beta-lactose molecule in g53a6. Following are
the steps I followed.
1) Draw lactose in Avogadro
2) Use PRODRG to get ITP template
3) Change the charges and charge groups in accordance with Oostenbrink et al
2004 and Lins et al 2005.
4) Change the bonds and angles in accordance with Oostenbrink et al, which
matches Lins et al
5) Check the improper dihedrals for chiral centers
6) Set up the proper dihedrals using Lins et al.
7) Set the exclusion you mentioned here (between O5 and H1)
8) Change the C-C-C-O5 specification from Lins et al to CCCO1 specification
as in your post (explained below)
This gives the following charges and dihedrals:
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 LAT O2 1 -0.642 15.9994
2 H 1 LAT H2 1 0.410 1.0080
3 CH1 1 LAT C2 1 0.232 13.0190
4 CH1 1 LAT C3 2 0.232 13.0190
5 OA 1 LAT O3 2 -0.642 15.9994
6 H 1 LAT H3 2 0.410 1.0080
7 CH1 1 LAT C4 3 0.232 13.0190
8 OA 1 LAT O4 3 -0.642 15.9994
9 H 1 LAT H4 3 0.410 1.0080
10 CH1 1 LAT C5 4 0.376 13.0190
11 CH2 1 LAT C6 5 0.232 14.0270
12 OA 1 LAT O6 5 -0.642 15.9994
13 H 1 LAT H6 5 0.410 1.0080
14 OA 1 LAT O5 4 -0.480 15.9994
15 CH1 1 LAT C1 4 0.232 13.0190
16 OA 1 LAT O1 4 -0.360 15.9994
17 CH1 1 LAT C4' 4 0.232 13.0190 ;'
18 CH1 1 LAT C3' 6 0.232 13.0190 ;'
19 OA 1 LAT O3' 6 -0.642 15.9994 ;'
20 H 1 LAT H3' 6 0.410 1.0080
21 CH1 1 LAT C2' 7 0.232 13.0190 ;'
22 OA 1 LAT O2' 7 -0.642 15.9994 ;'
23 H 1 LAT H2' 7 0.410 1.0080
24 CH1 1 LAT C1' 8 0.232 13.0190 ;'
25 OA 1 LAT O1' 8 -0.538 15.9994 ;'
26 H 1 LAT H1' 8 0.410 1.0080
27 OA 1 LAT O5' 8 -0.480 15.9994 ;'
28 CH1 1 LAT C5' 8 0.376 13.0190 ;'
29 CH2 1 LAT C6' 9 0.232 14.0270 ;'
30 OA 1 LAT O6' 9 -0.642 15.9994 ;'
31 H 1 LAT H6' 9 0.410 1.0080
[ dihedrals ]
2 1 3 15 1 gd_30
; 2 1 3 4 1 gd_30
1 3 15 16 1 gd_18
; 1 3 15 14 1 gd_18
1 3 4 5 1 gd_18
1 3 4 7 1 gd_17
; 3 15 16 17 1 gd_29
3 15 14 10 1 gd_29
3 4 5 6 1 gd_30
3 4 7 8 1 gd_17
3 4 7 10 1 gd_34
15 3 4 7 1 gd_34
15 3 4 5 1 gd_17
16 15 3 4 1 gd_17
16 15 3 4 1 gd_34
14 15 3 4 1 gd_17
; 14 15 3 4 1 gd_34
; 6 5 4 7 1 gd_30
5 4 7 8 1 gd_18
5 4 7 10 1 gd_17
4 7 8 9 1 gd_30
4 7 10 11 1 gd_34
4 7 10 14 1 gd_17
; 4 7 10 14 1 gd_34
; 9 8 7 10 1 gd_30
8 7 10 11 1 gd_17
; 8 7 10 14 1 gd_18
; 7 10 11 12 1 gd_1
7 10 14 15 1 gd_29
13 12 11 10 1 gd_30
12 11 10 14 1 gd_3
12 11 10 14 1 gd_35
; 11 10 14 15 1 gd_29
14 15 16 17 1 gd_2
14 15 16 17 1 gd_32
15 16 17 18 1 gd_30
; 15 16 17 28 1 gd_29
16 17 18 19 1 gd_18
16 17 18 21 1 gd_17
16 17 28 29 1 gd_17
; 16 17 28 27 1 gd_18
; 17 18 19 20 1 gd_30
17 18 21 22 1 gd_17
17 18 21 24 1 gd_34
; 17 28 29 30 1 gd_17
17 28 27 24 1 gd_29
19 18 17 28 1 gd_17
18 17 28 29 1 gd_34
18 17 28 27 1 gd_17
; 18 17 28 27 1 gd_34
21 18 17 28 1 gd_34
20 19 18 21 1 gd_30
19 18 21 22 1 gd_18
19 18 21 24 1 gd_17
; 18 21 22 23 1 gd_30
18 21 24 25 1 gd_17
18 21 24 25 1 gd_34
18 21 24 27 1 gd_17
; 18 21 24 27 1 gd_34
23 22 21 24 1 gd_30
22 21 24 25 1 gd_18
; 22 21 24 27 1 gd_18
; 21 24 25 26 1 gd_30
21 24 27 28 1 gd_29
26 25 24 27 1 gd_2
26 25 24 27 1 gd_32
; 26 25 24 27 1 180.0 20.0 1 ; restrain?
http://compbio.biosci.uq.edu.au/atb/download.py?molid=2002
; 24 27 28 29 1 gd_29
27 28 29 30 1 gd_5
27 28 29 30 1 gd_37
28 29 30 31 1 gd_30
; 28 27 24 25 1 180.0 10.0 1
; Picked from Autieri et al J. Chem. Phys. 2010
; 10 7 4 5 1 180.0 2.4 2
; 15 3 4 5 1 180.0 2.4 2
; 4 3 15 16 1 180.0 0.5 2
; 11 10 14 15 1 180.0 0.5 2
; 7 4 3 1 1 180.0 0.5 2
; 28 17 18 19 1 180.0 2.4 2
; 24 21 18 19 1 180.0 2.4 2
; 18 21 24 25 1 180.0 0.5 2
; 29 28 27 24 1 180.0 0.5 2
; 17 18 21 22 1 180.0 0.5 2
[ exclusions ]
26 27
#The commented dihedrals are things I was trying#
The molecule starts giving off LINCS warnings during NVT or NPT
equilibration with a protein that I'm interested in. I have run just the
molecule alone to check if it's a problem with the complex, but the molecule
in water also gives the same error. The error is on the anomeric hydroxy
group on the reducing end of the molecule, namely glucose O1-H1. My
questions are:
1) In this post, you have set both gd_17 and gd_34 for C3-C2-C1-O1, while
Lins et al 2005 have set up gd_17 and gd_34 for C3-C4-C5-O5 or C3-C2-C1-O5.
My assumption is that Lins et al are treating the O5 as if it's a carbon
within the sugar ring. My chemistry is not good, but the O5 here is quite
different from that of the other oxygens and could require extra attention.
In the context of dihedrals, that's doubtful. Maybe on some quantum level there
is an important distinction, but not likely here. Take that up with the authors
of the force field itself ;)
I'm not sure why the O1 is treated like this in your post. Is it because
it's in a polymer? Also I noticed that you did not have the extra gd_34
definition for the dihedrals involving the O5, was it left out on purpose?
The building blocks I made were derived directly from what was available in the
53A6 force field. As I recall, everything else matched aside from what I added.
I'll leave that as an exercise to you to determine. I did simple diagnostic
simulations to verify stability, nothing more.
2) I realize that there are different ways to set the dihedrals for complete
coverage of the molecule (i. e. C2-C3-O3-H3/C4-C3-O3-H3). Is there any down
side to defining all of the possible dihedrals redundantly?
If you define multiple dihedrals for a given bond, they are summed together to
give the final term. Unless you have specific reason to do that, don't.
3) I realize that the topology you've shown here is a template, but have you
simulated this template successfully?
Yes.
I have run 1'-deoxy-1'-methoxylactose (replacing the glucose OH with a
terminal methoxy {according to the specifications from Lins et al} ) and it
doesn't give LINCS warnings. I haven't made any quality checks, but this
actually runs. So this simple change makes me think that the problem is not
anything else but this anomeric OH termination.
Other notes: running gmx v4.5.5, spc water, em run until Fmax <100
I'm sorry if I rambled on. This is the first molecule I'm parameterizing.
Please let me know if I made any careless mistakes or if there are other
lit. articles I should have taken into account.
Why not try using ATB to build the topology?
http://compbio.biosci.uq.edu.au/atb/
I think the results should be vastly more reliable than trying to
reverse-engineer a faulty PRODRG topology. They also have a reasonably large
database of building block molecules with which you can check your work.
-Justin
--
========================================
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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