[gmx-users] Catenation error

[suniba]

Hello experts and users

I have performed 4 simulations of same system starting with different initial 
conformations. Now when I am trying to catenate the trajectories with gmc 
trjcat, It is showing error that can’t catenate multiple trajectories with 
different number of atoms. I am not sure why the atom number is different since 
the system is same in all cases. 
With Regards
Suniba
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Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 159, Issue 125

[suniba shuaib]

*Hi all,>> I am calculating the RDF from a particular residue to a
particular> glycine molecule. I created an index file for both to do this.
My> simulation box is 1.5nm, but the RDF values are in the range of
2nm-3nm.> I have viewed my trajectory and all the components stay inside
the box.> Please could someone tell me how to overcome this issue? My
command line> is below:>> gmx rdf -f output.xtc -s input.tpr -n index.ndx
-o rdf.xvg -b 0 -e 6> -ref -sel -bin 0.5 -norm rdf>> Akash> --*

*Hi *
*Akash*
*Are you sure your simulation box is 1.5 nm? This sounds bit strange and
too small. What is the length of your protein or no. of amino acids. I am
afraid you are talking about the distance from edge to protein is 1.5nm. *

*Regards*
*Suniba*

On Mon, Jul 31, 2017 at 1:58 PM, <
gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>1. Re: Question on force field (YanhuaOuyang)
>2. gmx mdmat calculation of heavy atoms of two side chains
>   (? ?)
>3. RDF Values (Pandya, Akash)
>4. Re: RDF Values (saima kalsoom)
>5. hole in the simulation box (edesantis)
>6. Re: RDF Values (sp...@iacs.res.in)
>
>
> --
>
> Message: 1
> Date: Mon, 31 Jul 2017 10:54:37 +0800 (CST)
> From: YanhuaOuyang <15901283...@163.com>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Question on force field
> Message-ID: <18244f50.3a1e.15d969118bb.coremail.15901283...@163.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Justin,  Thank you very much. I get it now.Best
> regards,Ouyang
> At 2017-07-31 10:46:10, "Justin Lemkul" <jalem...@vt.edu> wrote:
> >
> >
> >On 7/30/17 8:58 PM, YanhuaOuyang wrote:
> >> Hi,
> >>   I have run a protein MD simulation and choose a force field "8:
> CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) ". I wonder
> that whether the CHARMM27 all-atom force field here is equal to the
> CHARMM22/CMAP
> >>
> >
> >Well, not "equal" but it means that the "CHARMM27" files include C22/CMAP
> for
> >proteins.  There is no such thing as a CHARMM27 protein force field.  The
> C27
> >nucleic acid and lipid parameters came out at the same time as the
> C22/CMAP
> >protein force field, and got somewhat unfortunately lumped together in
> nomenclature.
> >
> >-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
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> >* Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>
> --
>
> Message: 2
> Date: Mon, 31 Jul 2017 14:19:07 +0900
> From: ? ?   <b.mijidd...@gmail.com>
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] gmx mdmat calculation of heavy atoms of two side
> chains
> Message-ID:
> <CABgRApuA3d+Vi=XzoBshixqXOypvPx0Ady0bP_aoE0p3O7JFzw@mail.
> gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear gmx users,
>
> I would like to know about the hydrophobic interaction between heavy atoms
> of side chains in different chains of peptide

[gmx-users] amino acid topology

[suniba shuaib]

Hello users and experts
I want to know if I can use gmx x2top for generating topology of a modified
amino acid linked with a natural peptide sequence?
or in general topology of a small molecule?

Thank You
Suniba
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[gmx-users] Catenation and sampling

[suniba shuaib]

Dear users and experts

I have simulated a protein in water using OPLS-AA force field. Initially I
performed a 5 ns simulation and then extracted frames out of it e.g. at
1ns, 2ns, 3ns etc. and then performed simulation for 100 ns of each
extracted frame. Now I have five 100 ns trajectories (A.xtc, B.xtc, C.xtc
etc..). My question is how should I catenate these trajectories in order to
ensure good sampling. When I used gmx trjcat with -settime flag, I obtained
RMSD and Rg which showed very high fluctuation till 150 ns and then was
quiet stable till the end of 500ns. I am confused if these extra high
fluctuations are due to poor sampling or improper catenation. Please help
me.

The fluctuations in RMSD were between 0.2-1.8 nm till 150 ns and then RMSD
stayed between 1.0-1.1 nm.

With Regards
Suniba
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[gmx-users] Bond lengths

[suniba shuaib]

Dear Users
I have performed a 200 ns MD simulation of a protein and a small molecule
inhibitor of 30 atoms, using GROMOS 43a1 ff and Gromacs v 5.0. Taking
reference from a number of papers and similar systems, I have used LINCS
algorithm to constrain all bond lengths.
I have reported interactions like pi-pi and hydrogen bonding between
protein and ligand plus some other analysis and  recently i submitted my
article. Reviewers have asked few question one of which is:

*Q: Why you have constrained all bond lengths? A good force field should
permit free variation of the bond lengths and only high frequency motions
(C-H) should be constrained.*

As i visited mailing list, I found an answer by Justin Lemkul:

*"The effects of H-bond vibrations aren't of interest for the problems
at hand; if you want to model bond formation, you can't accept a model
that has no "electron vibrations," and *that* drives your choice of
time step."*

Another reply by Mark Abraham:
"*Force field parameters are (unfortunately) co-optimized with and
dependent on*

*implementation issues like size of time step and lengths of cut-offs. The
use of constraints=all-bonds couples constraints across a whole polymer; if
that's a protein simulated using a spatial domain decomposition, those
atoms are widely distributed on the machine and the communication required
for the iterative constraint solver can become rate limiting at extreme
scale. Reducing the constraint iteration to a single node is unattractive
if the rest of the machine lies idle - which is part of why we'd like to
improve the ability to deploy task parallelism in GROMACS at scale. The
main alternative is using shorter time steps (maybe no constraints at all!)
- if they only way you can get 10x greater sampling rate for a single
simulation is by using 100x the hardware at one tenth of the time step,
then that could be a serious option.

I think that feeling that "constrained H bonds" is natural and "constrained
heavy-atom bonds" is artificial is wrongly conflating experience with
correctness."*


After reading these answers, I am little confused how should i respond
to the raised question. In my case, I believe, it was not necessary to
keep the system unconstrained. Plus, from Mark's answer, I concluded
that it is better to keep all bonds constrained? Please clear my
confusion.

Thank You

Suniba
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[gmx-users] Catenation and Visualization

[suniba]

Hello everyone
I have completed two independent 100 ns simulations of two differnt proteins in 
water. One is monomer and the other is trimer. Both simulations were allowed to 
run for 50 ns intially, after visulation, trajectories were 'correct' and then 
extended the simulation to 100 ns. Now after completion and catenation, when i 
converted the .xtc into movie.pdb using trjconv, the molecule seems broken in 
all the frames and i am not able to view it in cartoon style. Moreover, when i 
load the .pdb file of monomer or trimer in Pymol, Always two files are getting 
uploaded. I dont know what is the other file but it remains 'static' when i 
play the movie. Is this visualization problem or i madd a mistake in 
catenation? Can someone plz give insight
With Regards

Sent from my iPhone
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Re: [gmx-users] on md of protein-ligand

[suniba]

I believe gromacs will not "find out" the bindig site, neither the servers. You 
have to make it sure. And ATB gives 56A3 and 54A7 files; any of Gromos ff 
parameters can be interconverted with slight minor modifications. For other 
ffs, very good servers are specified by Justin in his tutorial. 
Best wishes
Suniba

Sent from my iPhone

> On 19-Apr-2016, at 5:43 pm, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
>> On 4/19/16 8:10 AM, Brett wrote:
>> Dear All,
>> 
>> 
>> It seems the external servers preparing the ligand files (antechamber for 
>> example) not only optimize the coordinates of the ligands, but it changes 
>> the ligand from one place to another place, thus the ligand coordinates by 
>> the external server cannot occupy the ligand binding pocket in the original 
>> protein-ligand complex.
>> 
>> 
>> I am looking forward to getting a reply from you on how to have the external 
>> server processed ligand find the ligand binding pocket in the protein-ligand 
>> complex for md.
> 
> Topology-generating servers aren't going to "find the ligand binding pocket" 
> - your job is to make sure the original coordinates are preserved, as the 
> previous message has instructed you on how to do.
> 
> -Justin
> 
>> 
>> Brett
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> At 2016-04-19 19:44:23, "suniba" <sun.i...@gmail.com> wrote:
>>> After pdb2gmx, protein topology is prepared. You prepare the ligand 
>>> topology from an external server or parametrize it. Then you prepare 
>>> complex.gro and include the ligand topology manually in topol.top (topology 
>>> generated by pdb2gmx). And for your second question, I used ATB today and 
>>> realized that one should always use "original geometry" co-ordinates as 
>>> 'optimized geometry' will/may cause clashes with protein etc.. So, avoid 
>>> PRODRG server and use ATB and then download the co-ordinates and .itp of 
>>> original geometry. Rest process is same as mentioned in tutorial.
>>> Regards
>>> 
>>> Sent from my iPhone
>>> 
>>>> On 19-Apr-2016, at 4:58 pm, Brett <brettliu...@163.com> wrote:
>>>> 
>>>> Dear All,
>>>> 
>>>> 
>>>> I am learning the md of protein-ligand based on the Justin on-line 
>>>> tutorial. My first question is, for the topology files we need to produce 
>>>> the protein part and ligand part separately, and the input for pdb2gmx did 
>>>> not contain the ligand part. After I got the ligand files, I find the 
>>>> coordinate of the ligands was different from the ligand pdb in the 
>>>> protein-complex pdb (although the rmsd between the ligand topology and the 
>>>> ligand in the complex was 0). Then during md process how does GROMCS know 
>>>> where is the position of the ligand in the complex?
>>>> 
>>>> 
>>>> Correspondingly, my second question is, suppose I have a protein dimer 
>>>> with 2 identical subunits, 1 subunit was a cAMP binding, and 1 was apo. 
>>>> Then during the md process how does GROMACS know which subunit binding 
>>>> with the cAMP and which subunit was apo?
>>>> 
>>>> 
>>>> I am looking forward to getting a reply from you.
>>>> 
>>>> 
>>>> Brett
>>>> --
>>>> Gromacs Users mailing list
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>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>>> 
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>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at 
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>> 
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> 
> -- 
> ==
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceut

Re: [gmx-users] Molecule not minimized and NVT failure

[suniba]

Thank you Mark and Justin, problem is solved with ATB. 
Regards

Sent from my iPhone

> On 18-Apr-2016, at 9:36 pm, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
>> On 4/18/16 12:02 PM, suniba wrote:
>> 
>> Hello users I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0.
>> Therefore, following Justin's tutorial, I used PRODRG for ligand topolgy. I
> 
> After doing my tutorial, you should *not* be using PRODRG for topologies, for 
> the reasons mentioned in that very tutorial.
> 
>> have drawn ligand using chemdraw and minimized the structure using chem3D.
>> However, during energy minimization step in gromacs, the values converge
>> earlier after 490 steps of minimization. This means that structure is not
>> energy minimized properly. Also, during NVT, it crashes very early giving a
> 
> The number of steps has nothing to do with whether or not EM was effective.
> 
>> LINCS warning which is posted frequently in mailing list and the 'water'
>> molecule not settled error. I have gone through all the solutions and
>> according to my knowledge, the problem is with minimization. I am confused
>> now how to minimize the structure properly to avoid the error. The long bond
>> warning might also arise due to bad minimization? Any suggestions please. If
>> require I can paste the ligand co-ordinates.
> 
> Ligand coordinates will tell us nothing of use.  The topology is more 
> instructive, but in general go through: 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
> 
> If your topology is straight from PRODRG, that's suspect #1 on my list.
> 
> -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
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Re: [gmx-users] on md of protein-ligand

[suniba]

After pdb2gmx, protein topology is prepared. You prepare the ligand topology 
from an external server or parametrize it. Then you prepare complex.gro and 
include the ligand topology manually in topol.top (topology generated by 
pdb2gmx). And for your second question, I used ATB today and realized that one 
should always use "original geometry" co-ordinates as 'optimized geometry' 
will/may cause clashes with protein etc.. So, avoid PRODRG server and use ATB 
and then download the co-ordinates and .itp of original geometry. Rest process 
is same as mentioned in tutorial. 
Regards

Sent from my iPhone

> On 19-Apr-2016, at 4:58 pm, Brett  wrote:
> 
> Dear All,
> 
> 
> I am learning the md of protein-ligand based on the Justin on-line tutorial. 
> My first question is, for the topology files we need to produce the protein 
> part and ligand part separately, and the input for pdb2gmx did not contain 
> the ligand part. After I got the ligand files, I find the coordinate of the 
> ligands was different from the ligand pdb in the protein-complex pdb 
> (although the rmsd between the ligand topology and the ligand in the complex 
> was 0). Then during md process how does GROMCS know where is the position of 
> the ligand in the complex?
> 
> 
> Correspondingly, my second question is, suppose I have a protein dimer with 2 
> identical subunits, 1 subunit was a cAMP binding, and 1 was apo. Then during 
> the md process how does GROMACS know which subunit binding with the cAMP and 
> which subunit was apo?
> 
> 
> I am looking forward to getting a reply from you.
> 
> 
> Brett
> -- 
> Gromacs Users mailing list
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Re: [gmx-users] Molecule not minimized and NVT failure

[suniba]

Thank you Justin, I understand the problems with PRODRG. I am switching to ATB 
now but earlier, I performed similar study with different ligand using PRODRG, 
and corrected charges according to the mentioned paper. No problem occured at 
all. I understand all systems are different. I was surprised as the ligand is a 
very simple molecule. Anyhow, now I will rerun using ATB and will contact if 
the problem persists. 
Thank you
Suniba

Sent from my iPhone

> On 18-Apr-2016, at 9:36 pm, Justin Lemkul <jalem...@vt.edu> wrote:
> 
> 
> 
>> On 4/18/16 12:02 PM, suniba wrote:
>> 
>> Hello users I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0.
>> Therefore, following Justin's tutorial, I used PRODRG for ligand topolgy. I
> 
> After doing my tutorial, you should *not* be using PRODRG for topologies, for 
> the reasons mentioned in that very tutorial.
> 
>> have drawn ligand using chemdraw and minimized the structure using chem3D.
>> However, during energy minimization step in gromacs, the values converge
>> earlier after 490 steps of minimization. This means that structure is not
>> energy minimized properly. Also, during NVT, it crashes very early giving a
> 
> The number of steps has nothing to do with whether or not EM was effective.
> 
>> LINCS warning which is posted frequently in mailing list and the 'water'
>> molecule not settled error. I have gone through all the solutions and
>> according to my knowledge, the problem is with minimization. I am confused
>> now how to minimize the structure properly to avoid the error. The long bond
>> warning might also arise due to bad minimization? Any suggestions please. If
>> require I can paste the ligand co-ordinates.
> 
> Ligand coordinates will tell us nothing of use.  The topology is more 
> instructive, but in general go through: 
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
> 
> If your topology is straight from PRODRG, that's suspect #1 on my list.
> 
> -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 
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Re: [gmx-users] Molecule not minimized and NVT failure

[suniba]

Hi Mark
I corrected the PRODRG charges according to the paper cited in tutorial. The 
final energy after EM was -5.6. Anyhow, I will visualize em results and then 
see what happens. 
Thank you

Sent from my iPhone

> On 18-Apr-2016, at 9:37 pm, Mark Abraham <mark.j.abra...@gmail.com> wrote:
> 
> Hi,
> 
> The number of EM steps doesn't mean anything. The final energy can suggest
> that something sensible happened, but the values depend on what your system
> has in it. You also should visualize the result of the EM and see if that
> fits with your chemical knowledge. PRODRG charges often won't produce
> sensible results.
> 
> Mark
> 
>> On Mon, Apr 18, 2016 at 6:03 PM suniba <sun.i...@gmail.com> wrote:
>> 
>> 
>> Hello users
>> I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0. Therefore,
>> following Justin's tutorial, I used PRODRG for ligand topolgy. I have drawn
>> ligand using chemdraw and minimized the structure using chem3D. However,
>> during energy minimization step in gromacs, the values converge earlier
>> after 490 steps of minimization. This means that structure is not energy
>> minimized properly. Also, during NVT, it crashes very early giving a LINCS
>> warning which is posted frequently in mailing list and the 'water' molecule
>> not settled error. I have gone through all the solutions and according to
>> my knowledge, the problem is with minimization. I am confused now how to
>> minimize the structure properly to avoid the error. The long bond warning
>> might also arise due to bad minimization? Any suggestions please. If
>> require I can paste the ligand co-ordinates.
>> 
>> With Regards
>> Suniba
>> Sent from my iPhone
>> --
>> 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
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[gmx-users] Molecule not minimized and NVT failure

[suniba]

Hello users
I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0. Therefore, 
following Justin's tutorial, I used PRODRG for ligand topolgy. I have drawn 
ligand using chemdraw and minimized the structure using chem3D. However, during 
energy minimization step in gromacs, the values converge earlier after 490 
steps of minimization. This means that structure is not energy minimized 
properly. Also, during NVT, it crashes very early giving a LINCS warning which 
is posted frequently in mailing list and the 'water' molecule not settled 
error. I have gone through all the solutions and according to my knowledge, the 
problem is with minimization. I am confused now how to minimize the structure 
properly to avoid the error. The long bond warning might also arise due to bad 
minimization? Any suggestions please. If require I can paste the ligand 
co-ordinates.

With Regards
Suniba
Sent from my iPhone
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Re: [gmx-users] Modified peptides

[suniba]

Thank you very much Dr. Lemkul

Sent from my iPhone

> On 02-Apr-2016, at 10:34 pm, Justin Lemkul  wrote:
> 
> 
> 
>> On 4/2/16 2:11 AM, sun wrote:
>> Hello Gromacs Users I have already posted this query but in the absence of
>> any suggestion, I am posting it again. I hope someone will help me. I am
>> going to do protein-peptide MD using Justin's protein-ligand tutorial (ff
>> gromos43A1, GROMACS version 5.0). My ligand is a pentameric modified peptide.
>> In the tutorial, I studied that Gromos96 parameters are obtained from PRODRG
>> server but due to less uniformity in charges, it is not 100% reliable. Its
>> allright, Charges can be corrected from the paper that is cited in tutorial.
>> But, I have also read that for modified peptides or sequences, we can make
>> changes in force fields manually. So, my query is, which option would be more
>> suitable for my peptide? Is it OK to obatin co-ordinates for modified amino
>> acid from PRODRG?
> 
> You don't need PRODRG at all, really, but sure, you can use coordinates.
> 
> The proper answer is to parametrize the residue in a manner consistent with 
> the parent force field.  The downside to GROMOS force fields is that, while 
> the functional groups are generally quite transferable, coming up with new 
> parameters is hard.  The published papers do not give many methodological 
> details, rather emphasizing the empirical nature of the force field.  This 
> implies that one needs an intuitive sense of how to parameterize new species, 
> which is both frustrating to new users and unsatisfying in a rigorous sense. 
> Force fields like CHARMM, AMBER, and OPLS-AA have very easy-to-follow, 
> logical progression from QM calculations for initial electrostatic parameters 
> and internal terms, to empirical refinement based on very well defined 
> criteria.
> 
> -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
> 
> ==
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