Re: [gmx-users] Fix the residues

[Amir Zeb]

Is TYR and SER are N-terminal and C-terminal residues , respectively?
Also, you may compare the corresponding atoms of each residues with same
residues present in your system and does not show the mentioned warning.

All the best

On Fri, Jan 6, 2017 at 10:58 AM, liming_52  wrote:

> Dear Gromacs users,
>
> I am trying to run a md using 4n6p.cif, which was obtained from PDB. I
> converted the file into pdb format using DS4.1, and got the file named
> lactoferrin.pdb. When I directly run
> the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water
> spce", the program runs and produces the information as follows:
> ...
> WARNING: WARNING: Residue 1 named TYR of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> WARNING: WARNING: Residue 335 named SER of a molecule in the input file
> was mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> ...
> How should I fix the residues? And which tools should I use? Is there any
> examples or tutorials?
>
> If anyone can suggest a solution to this issue, it would be really helpful.
>
>
>
>
>
>
>
> --
>
> With my best wishes,
> Ming Li, PhD
> Chinese Academy of Agricultural Sciences, Beijing, China
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Regarding calculation of diffusion constant (through MSD) of solvent molecules near protein surface

[Apramita Chand]

Dear All,
Say I want to calculate how the water molecules near the surface of protein
are diffusing, how would I do that?
Say I look at some hydrogen bonding interactions using VMD and zoom in and
identify the SOL molecules around the surface . Can I create an index file
containing those particular SOL molecules and calculate their diffusion?
Would this work or is there another proper way to do it than just
identifying such solvent molecules visually?


Thanks,

Regards
Apramita
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Topology parameters for ligand

[tasneem kausar]

I got it.

I have looked at the input files for the T4-lysozyme tutorial available at
alchemistry.org. They have defined state A and state B. I am using
GROMACS-5.1.4 for these calculation. So as mentioned in gromacs manual
decoupling parameters are taken from the mdp options, like by defining
[lambda-moltype] in mdp file. As I know from the tutorials and manual the
solvation free energy of the ligand can calculated.

>From the alchemistry.org input files, the topology parameters of ligand are
inserted in protein topology named as complex.top.

If I follow the same protocol without defining the state B of the ligand in
topology, how the ligand molecule will be decoulped in complex.



On Sun, Jan 8, 2017 at 10:21 PM, Justin Lemkul  wrote:

>
>
> On 1/7/17 10:29 PM, tasneem kausar wrote:
>
>> Thank you for your reply
>>
>> In last section of your tutorial you have suggested some changes to made
>> in
>> mdp file. That can be used for solvation free energies.
>> For free energy calculation of protein drug complex, is it only lambda
>> restraint to be defined?
>>
>>
> Along with a complex system of [intermolecular_interactions] that preserve
> the relative orientation of the ligand.  This is a very complex calculation
> in practice.  See examples on alchemistry.org and in the literature in
> works by Roux, Im, Karplus, etc.  My tutorial is not very useful for such
> calculations; it is extremely basic relative to what is needed to carry out
> a binding free energy calculation.  I only mentioned it there because so
> many people asked about it and I wanted to clear up any confusion.
>
> -Justin
>
>
> On 8 Jan 2017 01:45, "Justin Lemkul"  wrote:
>>
>>
>>>
>>> On 1/7/17 6:05 AM, tasneem kausar wrote:
>>>
>>> Dear all

 I am following Justin's tutorial methane in water for free energy
 calculation. I am using Gromacs-5.1.4. The charges of methane in
 topology
 are set to zero. So following the same protocol, is it relevant to set
 the
 charges at zero in topology of the drug. I am confused because in
 tutorial
 of Sander (ethanol in water) charges are present in the topology file.

 Please tell me the difference in both the tutorials and how can I apply
 it
 to drug that I want to study.


 The charges in my tutorial are set to zero because the stated goal of
>>> that
>>> tutorial is to reproduce *only the LJ portion of the hydration free
>>> energy*
>>> to match a published paper.  This creates a very simple, robust system.
>>> If
>>> you want to calculate a real, meaningful hydration or binding free
>>> energy,
>>> charge transformation is required.
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> 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
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> 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
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Mycobacterium cell wall protein

[Shanmuga Priya V.G]

Dear Gromacs Users,
I have a insilico model of Mycobacterium tuberculosis cell wall  (surface)
protein
which has no transmembrane helices. Which Gromacs tutorials should I
follow for MD studies to know about its conformational stability and
latter for protein - ligand studies. Kindly guide me

Thanking you

with regards
V.G.Spriya

KLE Dr.MSSCET,Belgaum
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Protein-ligand complex simulation

[Nivedita Rai]

Dear Gromacs User,

I am running *protein ligand complex* simulation by
following the Beven lab tutorial. while production run im getting two notes
such as:

NOTE 1 [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Number of degrees of freedom in T-Coupling group Protein_UNK is 8298.87
Number of degrees of freedom in T-Coupling group Water_and_ions is 180606.12
Largest charge group radii for Van der Waals: 0.267, 0.265 nm
Largest charge group radii for Coulomb:   0.267, 0.265 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.118 0.118 0.118
Estimate for the relative computational load of the PME mesh part: 0.32

NOTE 2 [file md.mdp]:
  This run will generate roughly 5681 Mb of data

Is *note1* will create any trouble? if yes then how to rectify it?

-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Free energy calculation of protein and drug

[Amir Zeb]

Hello Tasneem,

Same like you, I'm pretty new to this field too. I don't know enough how to
calculate free energy in gromacs. I did only MM/PBSA for binding energy
calculations.
I'll let you know if i get some thing relevant to your question.

All the best.

Thanks

On Thu, Jan 5, 2017 at 10:28 PM, tasneem kausar 
wrote:

> Dear all
>
> It is first time I am calculating free energy of protein and ligand. I am
> following the Justin's tutorial of methane in water free energy
> calculations. Though only van der waal lambda are defined so I have taken
> the mdp files from the alchemistry.org web page. Since the ligand and
> protein under my study have positive charges (one positive charge on ligand
> and tree positive charges on protein). So I have to add a CL ions in
> topology file to make a neutral sytem.
> Is it okay to use the system with ion for free energy calculation?
> If yes, What are change that can be made in mdp entry.
>
> Waiting for suggestions
> Thanks in Advance
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] pulling protein-ligand complex

[abhisek Mondal]

Sincere apologies...
I have uploaded the files here...
https://drive.google.com/drive/folders/0B6O-L5Y7BiGJT29hSGlEWTM3Zk0?usp=sharing

I'm running another pull experiment with "pull_rate1 =0.01".


On Sun, Jan 8, 2017 at 10:23 PM, Justin Lemkul  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  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  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  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
 Group10 (Prot-Masses) has  1693 elements
 Group11 (non-Protein) has 2646618 elements
 Group12 (  Other) has15 elements
 Group13 (JZ4) has15 elements
 Group14 ( NA) has  1602 elements
 Group15 ( CL) has  1608 elements
 Group16 (  Water) has 2643393 elements
 Group17 (SOL) has 2643393 elements
 Group18 (  non-Water) has  4918 elements
 Group19 (Protein_chain_A) has  3210 

Re: [gmx-users] pulling protein-ligand complex

[Justin Lemkul]

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  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  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  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
Group10 (Prot-Masses) has  1693 elements
Group11 (non-Protein) has 2646618 elements
Group12 (  Other) has15 elements
Group13 (JZ4) has15 elements
Group14 ( NA) has  1602 elements
Group15 ( CL) has  1608 elements
Group16 (  Water) has 2643393 elements
Group17 (SOL) has 2643393 elements
Group18 (  non-Water) has  4918 elements
Group19 (Protein_chain_A) has  3210 elements
Group20 (JZ4) has15 elements
Group21 ( NA) has  1602 elements
Group22 ( CL) has  1608 elements
Group23 ( Water_and_ions) has 2646603 elements
Group24 (r_1-163) has  5605 elements
Group25 (  r_164) has39 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 
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 
wrote:





On 1/7/17 2:51 PM, abhisek Mondal wrote:



Hi,

I'm pulling ligand out of protein using umbrella sampling 

Re: [gmx-users] Regarding gromacs commands..

[Justin Lemkul]

On 1/7/17 10:58 PM, Dilip H N wrote:

can i create it with Avogadro molecular editor software..??


Probably, but that's a question for whatever help forum they provide.


I tried creating using this software,, than if i compile it and run the
command of mdrun..
it is giving segmentation fault
how to rectify it..??



Not a clue.  There are a ton of steps between "create a PDB file" and "execute 
mdrun," none of which you've shown us.  If you want detailed help, you have to 
provide detailed information (steps taken, exact commands given, text of input 
files and what you're trying to accomplish, etc).  We can't read your mind.  A 
seg fault is a catastrophic failure of the physical model due to problems with 
any number of things.  It's not productive for anyone to guess.


-Justin




 Sent with Mailtrack


On Sat, Jan 7, 2017 at 12:15 AM, Justin Lemkul  wrote:




On 1/6/17 2:24 AM, Dilip H N wrote:


no...
I want to create  300 molecules of ammonia...



Well, you asked about BF3, so you got an answer about BF3 :)

how can i create  300 molecules of ammonia and then get it in .pdb file

format..??



For a simple molecule like NH3 you can easily write the coordinates by
hand from basic geometry.  Otherwise, find an NMR structure of a protein
that contains Lys and copy its NZ-HZ[123] group and use that.  gmx
insert-molecules -nmol 300 will give you a box of 300.

-Justin




 Sent with Mailtrack


On Fri, Jan 6, 2017 at 11:01 AM, Alex  wrote:

Google "bf3 rcsb" > third result from the top

https://www3.rcsb.org/ligand/BF3 > download cif file (view/download on
the right) > open in pymol > save as pdb

Alex


On 1/5/2017 10:20 PM, Dilip H N wrote:

I want to do a simulation of BF3 molecule..

how can i create a pdb file of BF3 molecule..??
is there any softwares for creating a .pdb files ..??



--

Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.







--
==

Justin A. Lemkul, Ph.D.
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

==

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.







--
==

Justin A. Lemkul, Ph.D.
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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Topology parameters for ligand

[Justin Lemkul]

On 1/7/17 10:29 PM, tasneem kausar wrote:

Thank you for your reply

In last section of your tutorial you have suggested some changes to made in
mdp file. That can be used for solvation free energies.
For free energy calculation of protein drug complex, is it only lambda
restraint to be defined?



Along with a complex system of [intermolecular_interactions] that preserve the 
relative orientation of the ligand.  This is a very complex calculation in 
practice.  See examples on alchemistry.org and in the literature in works by 
Roux, Im, Karplus, etc.  My tutorial is not very useful for such calculations; 
it is extremely basic relative to what is needed to carry out a binding free 
energy calculation.  I only mentioned it there because so many people asked 
about it and I wanted to clear up any confusion.


-Justin


On 8 Jan 2017 01:45, "Justin Lemkul"  wrote:




On 1/7/17 6:05 AM, tasneem kausar wrote:


Dear all

I am following Justin's tutorial methane in water for free energy
calculation. I am using Gromacs-5.1.4. The charges of methane in topology
are set to zero. So following the same protocol, is it relevant to set the
charges at zero in topology of the drug. I am confused because in tutorial
of Sander (ethanol in water) charges are present in the topology file.

Please tell me the difference in both the tutorials and how can I apply it
to drug that I want to study.



The charges in my tutorial are set to zero because the stated goal of that
tutorial is to reproduce *only the LJ portion of the hydration free energy*
to match a published paper.  This creates a very simple, robust system.  If
you want to calculate a real, meaningful hydration or binding free energy,
charge transformation is required.

-Justin

--
==

Justin A. Lemkul, Ph.D.
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

==
--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.



--
==

Justin A. Lemkul, Ph.D.
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

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] LJ Interaction between 2 groups looks unusual

[Mark Abraham]

Hi,

We can't see your figure, but as you would see in the mdrun log file,
energy groups are not implemented for gpu runs. You can do mdrun -nb cpu
-rerun however

Mark

On Sun, 8 Jan 2017 07:23 Mijiddorj Batsaikhan  wrote:

> Dear gmx users,
>
> I run 500 ns simulation using GPU. After simulation I made mdrun -rerun.
> Finally, I performed gmx energy analysis. Result looks unusual as a
> following figure. LJ Interaction between 2 groups.
>
> ​
>
> How is the figure? Is there any advice?
>
>
> Best regards,
>
> Mijiddorj
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.