On 1/9/17 9:20 AM, abhisek Mondal wrote:
Alright. But can you please tell me what is the strategy of defining a
pull-vec ? The standard tutorial does not tell anything about it, if I got
it right.
Can you provide me some basics regarding pull-vec ?
You have to choose a path along which to pull the two species apart. What that
is depends on the geometry of the system. For instance, you can define a pull
vector by simply calculating the difference in the COM of the ligand and a
subset of residues in the binding site and then calculating the connecting
vector, or you can rotate the system so that this vector lies along a convenient
Cartesian axis and use pull-dim instead of pull-vec, etc.
For the tutorial system it's quite easy because experiments have shown that
amyloid fibrils grow unidirectionally and therefore the reaction coordinate was
quite straightforward (see the associated paper). But that discussion is well
beyond what is required for a tutorial (unless you'd like to read lots of papers
about one specific biological system :)
-Justin
On Mon, Jan 9, 2017 at 6:32 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/8/17 12:34 PM, abhisek Mondal wrote:
Sincere apologies...
I have uploaded the files here...
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJT29hSGlE
WTM3Zk0?usp=sharing
I'm running another pull experiment with "pull_rate1 =0.01".
You probably need to define a more suitable vector for pulling. Your
current approach appears to accomplish nothing, and a faster pull rate will
not change that.
-Justin
On Sun, Jan 8, 2017 at 10:23 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/8/17 1:52 AM, abhisek Mondal wrote:
Alright. I'm attaching md_pull.mdp and sumary_distances.dat file.
May be I have set pulling rate very low. Anyway have a look.
The list does not accept attachments (if I had a nickel for every time I
said this...) so upload the files somewhere and provide a link.
-Justin
On Sun, Jan 8, 2017 at 6:03 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/7/17 5:20 PM, abhisek Mondal wrote:
It finished normally then. I got another question. I was pulling along
XZ
plane. Distances I got is not a arithmetic progression with respect to
different configurations. I mean the output looks like:
50 1.3637913
51 1.3729873
52 1.4363521
53 1.4652436
54 1.4503893
55 1.4260585
56 1.3836564
57 1.3918289
58 1.3942112
59 1.4296075
60 1.4574580
61 1.3772060
62 1.3604678
63 1.3986934
64 1.3650020
65 1.3965892
66 1.4247549
67 1.4097543
68 1.4460622
69 1.3933917
70 1.4080330
71 1.4576371
72 1.4678355
73 1.4853811
74 1.4144009
75 1.4365107
76 1.4342467
77 1.4353391
78 1.4025292
79 1.4092745
80 1.4392823
81 1.4330521
82 1.4404603
83 1.3839875
84 1.3936158
85 1.3747249
86 1.4166344
87 1.3945516
88 1.3606738
89 1.3709180
90 1.3676665
91 1.3724216
92 1.3779051
93 1.3530073
94 1.3227006
95 1.3054955
96 1.2701077
97 1.3492427
98 1.3388848
99 1.3286418
100 1.3590064
101 1.3886772
102 1.3654326
103 1.3153005
104 1.3110788
105 1.2885991
106 1.3051655
107 1.3151547
108 1.3163824
109 1.3328680
110 1.3280408
In such a case how am I to decide which ones to take as a starting
configurations ? Can you please give me an idea?
It would help to have a full explanation of what you're doing,
including
.mdp files. Getting partial details along the way makes it hard to
give
any useful advice.
It looks like your species just oscillated over a range of 0.1 nm,
which
achieves very little, if anything, and certainly nothing resembling
dissociation between the two.
-Justin
On Sun, Jan 8, 2017 at 2:34 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/7/17 3:59 PM, abhisek Mondal wrote:
yes. 19 and 20.
I have been able to modify distances.pl and it is running well I
guess.
It
is taking a little time per configuration to process.
Is there any way to know if distances.pl program terminates
normally
and
calculations are successful ?
You won't get error messages and you will get a data file with
distances
vs. configuration number.
-Justin
On Sun, Jan 8, 2017 at 2:20 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 1/7/17 3:36 PM, abhisek Mondal wrote:
Alright, I'm trying.
Please tell me one thing, given the fact I want to analyse the
protein-ligand pull scenario, what should be my choice during the
prompt i
get after executing "g_dist_mpi -s pull.tpr -f conf200.gro -n
index.ndx
-o
all"
Reading file pull.tpr, VERSION 4.6.2 (single precision)
Group 0 ( System) has 2648311 elements
Group 1 ( Protein) has 1693 elements
Group 2 ( Protein-H) has 1301 elements
Group 3 ( C-alpha) has 163 elements
Group 4 ( Backbone) has 489 elements
Group 5 ( MainChain) has 653 elements
Group 6 ( MainChain+Cb) has 805 elements
Group 7 ( MainChain+H) has 815 elements
Group 8 ( SideChain) has 878 elements
Group 9 ( SideChain-H) has 648 elements
Group 10 ( Prot-Masses) has 1693 elements
Group 11 ( non-Protein) has 2646618 elements
Group 12 ( Other) has 15 elements
Group 13 ( JZ4) has 15 elements
Group 14 ( NA) has 1602 elements
Group 15 ( CL) has 1608 elements
Group 16 ( Water) has 2643393 elements
Group 17 ( SOL) has 2643393 elements
Group 18 ( non-Water) has 4918 elements
Group 19 (Protein_chain_A) has 3210 elements
Group 20 ( JZ4) has 15 elements
Group 21 ( NA) has 1602 elements
Group 22 ( CL) has 1608 elements
Group 23 ( Water_and_ions) has 2646603 elements
Group 24 ( r_1-163) has 5605 elements
Group 25 ( r_164) has 39 elements
Do I go with System ? I only need to see protein-ligand pull
though.
What groups defined your reaction coordinate for the pulling?
Those
are
the groups you want.
-Justin
Can you give me some suggestions ?
On Sun, Jan 8, 2017 at 1:58 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 1/7/17 3:24 PM, abhisek Mondal wrote:
So I'm supposed to run "g_dist_mpi", right ? I'm on
gromacs-4.6.2.
If you're using an old version, the syntax is totally different,
so
you
will have to make lots of changes to the script (or not use it
at
all).
The catch here to analyze the COM distances between 2 pull
groups.
Am I
getting that right ?
Yes.
-Justin
On Sun, Jan 8, 2017 at 1:46 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 1/7/17 2:51 PM, abhisek Mondal wrote:
Hi,
I'm pulling ligand out of protein using umbrella sampling
method
in
gromacs-4.6.2.
Using "trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep"
command
generated
500 different files (selected "SYSTEM" in interactive prompt,
need
to
study
protein and ligand simultaneously). But when I use "perl
distances.pl
"
command I get none of the distances calculated.
Following output was generated:
...
Processing configuration 497...
Processing configuration 498...
Processing configuration 499...
Processing configuration 500...
readline() on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $distance in concatenation (.) or
string
at
distances.pl line 30.
readline() on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $distance in concatenation (.) or
string
at
distances.pl line 30.
readline() on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $distance in concatenation (.) or
string
at
distances.pl line 30.
readline() on closed filehandle IN at distances.pl line 16.
Use of uninitialized value $distance in concatenation (.) or
string
at
distances.pl line 30.
readline() on closed filehandle IN at distances.pl line 16.
...
Help me out here. What did go wrong ?
gmx distance failed. Run gmx distance yourself and see what
the
error
message is. The script just executes gmx distance and assumes
everything
works because it's designed for a tutorial. You may have to
modify
it
to
get it to work in your system; you can't assume it is
plug-and-play.
-Justin
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University of Maryland, Baltimore
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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