[gmx-users] gromacs.org_gmx-users Digest, Vol 187, Issue 21
pooja kesari
poojakesari10 at gmail.com
Mon Nov 11 10:53:17 CET 2019
Dear GMX users group
Message 4
> I am using GROMOS 43a force field, I have typed by protein and got the
> ligand file from PRODRG.
*Don't use PRODRG; its topologies are not of sufficient quality for running
MD simulations*.
How to generate ligand topology (GROMOS 43a force field)
Does your ligand have a +1 charge?
-Justin
My ligand does not have a charge. I simulated the same protein-ligand
complex for 10ns using GROMACS 5.1.4 on my standalone system. The server at
the institute has GROMACS 2018.1. I want to extend my simulation run now on
server.
----------------------------
> Dear All,
>
> I m trying to do a protein-ligand simulation,
> I am using GROMOS 43a force field, I have typed by protein and got the
> ligand file from PRODRG.
Don't use PRODRG; its topologies are not of sufficient quality for
running MD simulations.
> I prepared the complex and added solvent. *The protein has -8.0 charge by
> when i m neutralizing it only adds 7 positive charge.*
>
>
>
> * 3328 OM 336 VAL O1 1492 -0.635 15.9994 ;
> qtot -7.365 3329 OM 336 VAL O2 1492 -0.635
> 15.9994 ; qtot -8*
>
Does your ligand have a +1 charge?
-Justin
> When i added 8 positive charge using the below command
> gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL
> -np 8
>
>
>
>
>
>
>
> *[ molecules ]; Compound #molsProtein_chain_B 11IN
> 1SOL 22473NA 8*
>
> Again in the minimization step it is showing a list of
> *errors and warnings. *
> NOTE 1 [file em.mdp]:
> With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> that with the Verlet scheme, nstlist has no effect on the accuracy of
> your simulation.
>
> Setting the LD random seed to 787146813
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> Excluding 3 bonded neighbours molecule type '1IN'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'NA'
>
> NOTE 2 [file topol.top, line 21027]:
>
> *System has non-zero total charge: 1.000000 Total charge should normally
> be an integer. *See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> for discussion on how close it should be to an integer.
>
> WARNING 1 [file topol.top, line 21027]:
> *You are using Ewald electrostatics in a system with net charge*. This
can
> lead to severe artifacts, such as ions moving into regions with low
> dielectric, due to the uniform background charge. We suggest to
> neutralize your system with counter ions, possibly in combination with
a
> physiological salt concentration.
>
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are: 335 Protein residues
> There are: 1 Other residues
> There are: 22473 Water residues
> There are: 8 Ion residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 145023.00
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 80x80x80, spacing 0.113 0.113 0.113
> Estimate for the relative computational load of the PME mesh part: 0.20
> This run will generate roughly 6 Mb of data
>
> There were 2 notes
>
> There was 1 warning
> Please suggests how can overcome these errors.
Thanks & Regards,
Dr. Pooja Kesari
Post Doctoral Fellow
Department Of Biosciences and Bioengineering
Indian Institute of Technology Bombay
INDIA
On Fri, Nov 8, 2019 at 9:32 PM <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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>
> Today's Topics:
>
> 1. Re: Regarding multiple ligands' topology (Justin Lemkul)
> 2. Problem running simulation on gromacs 2018.8 version
> (pooja kesari)
> 3. Re: gmx trjorder (Christian Blau)
> 4. Re: Problem running simulation on gromacs 2018.8 version
> (Justin Lemkul)
> 5. Re: (no subject) (Christian Blau)
> 6. Re: (no subject) (shakuntala dhurua)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 8 Nov 2019 06:21:29 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding multiple ligands' topology
> Message-ID: <7fda6310-d8d4-2a53-c42f-9d700c3f6f49 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/8/19 2:38 AM, Mijiddorj B wrote:
> > Dear GMX users,
> >
> > I would like to use multiple small molecules in the simulation system.
> The
> > topology files of the ligands were generated by swissparam. However,
> grompp
> > could not recognize the second ligand topology during the preparation of
> > system and gives following message:
> > ########
> > '[ atomtypes ]'
> > Invalid order for directive atomtypes
> > ########
> >
> > How can overcome this problem?
>
>
> http://manual.gromacs.org/current/user-guide/run-time-errors.html#invalid-order-for-directive-xxx
>
> Combine all of the new atom types in one file that is #included in the
> correct order.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 8 Nov 2019 18:06:35 +0530
> From: pooja kesari <poojakesari10 at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Problem running simulation on gromacs 2018.8
> version
> Message-ID:
> <
> CAHxjgAGQDqj2x0-mqazAX7zMjGMRnqpnHOtKn+8XSzdYbJnm9g at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Dear All,
>
> I m trying to do a protein-ligand simulation,
> I am using GROMOS 43a force field, I have typed by protein and got the
> ligand file from PRODRG.
> I prepared the complex and added solvent. *The protein has -8.0 charge by
> when i m neutralizing it only adds 7 positive charge.*
>
>
>
> * 3328 OM 336 VAL O1 1492 -0.635 15.9994 ;
> qtot -7.365 3329 OM 336 VAL O2 1492 -0.635
> 15.9994 ; qtot -8*
>
>
> When i added 8 positive charge using the below command
> gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL
> -np 8
>
>
>
>
>
>
>
> *[ molecules ]; Compound #molsProtein_chain_B 11IN
> 1SOL 22473NA 8*
>
> Again in the minimization step it is showing a list of
> *errors and warnings. *
> NOTE 1 [file em.mdp]:
> With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> that with the Verlet scheme, nstlist has no effect on the accuracy of
> your simulation.
>
> Setting the LD random seed to 787146813
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> Excluding 3 bonded neighbours molecule type '1IN'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 1 bonded neighbours molecule type 'NA'
>
> NOTE 2 [file topol.top, line 21027]:
>
> *System has non-zero total charge: 1.000000 Total charge should normally
> be an integer. *See
> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> for discussion on how close it should be to an integer.
>
> WARNING 1 [file topol.top, line 21027]:
> *You are using Ewald electrostatics in a system with net charge*. This
> can
> lead to severe artifacts, such as ions moving into regions with low
> dielectric, due to the uniform background charge. We suggest to
> neutralize your system with counter ions, possibly in combination with a
> physiological salt concentration.
>
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are: 335 Protein residues
> There are: 1 Other residues
> There are: 22473 Water residues
> There are: 8 Ion residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> into groups...
> Number of degrees of freedom in T-Coupling group rest is 145023.00
> Calculating fourier grid dimensions for X Y Z
> Using a fourier grid of 80x80x80, spacing 0.113 0.113 0.113
> Estimate for the relative computational load of the PME mesh part: 0.20
> This run will generate roughly 6 Mb of data
>
> There were 2 notes
>
> There was 1 warning
> Please suggests how can overcome these errors.
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 8 Nov 2019 14:52:42 +0100
> From: Christian Blau <blau at kth.se>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gmx trjorder
> Message-ID: <9f734a77-33b7-449e-cebf-84983b205eda at kth.se>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hello Akash,
>
>
> Not knowing much more about your this system, this looks reasonable to me
> and should give you the count you just described.
>
>
> Best,
>
> Christian
>
> On 11/7/19 2:44 PM, Pandya, Akash wrote:
> > Hi,
> >
> > I would like to calculate the number of ligand molecules within 0.5 nm
> of a particular amino acid in my protein. I came across the gmx trjorder
> command (as shown below).
> >
> >
> > gmx trjorder -f Traj.gro -s Traj.tpr -n ProteinLIG.ndx -nshell
> nshell1.xvg -b 20000 -e 40000 -na 10 -r 0.5
> >
> >
> > I have 10 atoms in my ligand. I wanted to ask how accurate is this
> command in trying to calculate what I want?
> >
> >
> > Akash
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 8 Nov 2019 08:52:34 -0500
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Problem running simulation on gromacs 2018.8
> version
> Message-ID: <53533d16-c602-07a4-33ba-5f36554b6a1e at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 11/8/19 7:36 AM, pooja kesari wrote:
> > Dear All,
> >
> > I m trying to do a protein-ligand simulation,
> > I am using GROMOS 43a force field, I have typed by protein and got the
> > ligand file from PRODRG.
>
> Don't use PRODRG; its topologies are not of sufficient quality for
> running MD simulations.
>
> > I prepared the complex and added solvent. *The protein has -8.0 charge by
> > when i m neutralizing it only adds 7 positive charge.*
> >
> >
> >
> > * 3328 OM 336 VAL O1 1492 -0.635 15.9994 ;
> > qtot -7.365 3329 OM 336 VAL O2 1492 -0.635
> > 15.9994 ; qtot -8*
> >
>
> Does your ligand have a +1 charge?
>
> -Justin
>
> > When i added 8 positive charge using the below command
> > gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL
> > -np 8
> >
> >
> >
> >
> >
> >
> >
> > *[ molecules ]; Compound #molsProtein_chain_B 11IN
> > 1SOL 22473NA 8*
> >
> > Again in the minimization step it is showing a list of
> > *errors and warnings. *
> > NOTE 1 [file em.mdp]:
> > With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> > that with the Verlet scheme, nstlist has no effect on the accuracy of
> > your simulation.
> >
> > Setting the LD random seed to 787146813
> > Generated 279 of the 1225 non-bonded parameter combinations
> > Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
> > Excluding 3 bonded neighbours molecule type '1IN'
> > Excluding 2 bonded neighbours molecule type 'SOL'
> > Excluding 1 bonded neighbours molecule type 'NA'
> >
> > NOTE 2 [file topol.top, line 21027]:
> >
> > *System has non-zero total charge: 1.000000 Total charge should normally
> > be an integer. *See
> > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
> > for discussion on how close it should be to an integer.
> >
> > WARNING 1 [file topol.top, line 21027]:
> > *You are using Ewald electrostatics in a system with net charge*.
> This can
> > lead to severe artifacts, such as ions moving into regions with low
> > dielectric, due to the uniform background charge. We suggest to
> > neutralize your system with counter ions, possibly in combination
> with a
> > physiological salt concentration.
> >
> > Removing all charge groups because cutoff-scheme=Verlet
> > Analysing residue names:
> > There are: 335 Protein residues
> > There are: 1 Other residues
> > There are: 22473 Water residues
> > There are: 8 Ion residues
> > Analysing Protein...
> > Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> > into groups...
> > Analysing residues not classified as Protein/DNA/RNA/Water and splitting
> > into groups...
> > Number of degrees of freedom in T-Coupling group rest is 145023.00
> > Calculating fourier grid dimensions for X Y Z
> > Using a fourier grid of 80x80x80, spacing 0.113 0.113 0.113
> > Estimate for the relative computational load of the PME mesh part: 0.20
> > This run will generate roughly 6 Mb of data
> >
> > There were 2 notes
> >
> > There was 1 warning
> > Please suggests how can overcome these errors.
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 8 Nov 2019 15:00:54 +0100
> From: Christian Blau <blau at kth.se>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] (no subject)
> Message-ID: <37964cff-5b95-0e43-5274-1e04e9c30ae7 at kth.se>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Hello Shakuntala,
>
>
> If you already have the trajectories, you have to post-process at least
> once to filter the data down to a manageable
> size, and once to do the periodic boundary condition fix precisely as you
> described.
>
> If you set up a new simulation you may use "nstxout-compressed" to control
> the output frequency for your xtc file. It is
> very unlikely that you will need a .trr file, so you can even set nstxout,
> nstvout and nstfout to zero. Starting your
> post-processing from a xtc should speed up your analysis process.
>
>
> On another note: Please fill in a subject line in your emails, it makes it
> easier to search and keep track of the
> ongoing discussions.
>
>
> Best,
>
> Christian
>
>
> On 11/7/19 3:12 PM, shakuntala dhurua wrote:
> > I would like to calculate rmsd of protein system, but there is much time
> > taking for trjcat of all simulated trajectories (.trr file) then
> generated
> > .xtc file by using -center -pbc mol flag. from this .xtc file i use to
> > calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o .xvg I
> > want to ask here is any other way is available to directly calculate rmsd
> > without using trjcat or less time taking method.
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 8 Nov 2019 21:29:33 +0530
> From: shakuntala dhurua <madhu.dhurua94 at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] (no subject)
> Message-ID:
> <
> CAFXBQ7F-PaMwEWgzmEBhCaCY8wJw+-Krb-iCpb-ziMEK5YBjoQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Thank you sir for your suggestions
>
> On Fri, 8 Nov 2019, 7:31 pm Christian Blau, <blau at kth.se> wrote:
>
> > Hello Shakuntala,
> >
> >
> > If you already have the trajectories, you have to post-process at least
> > once to filter the data down to a manageable
> > size, and once to do the periodic boundary condition fix precisely as you
> > described.
> >
> > If you set up a new simulation you may use "nstxout-compressed" to
> control
> > the output frequency for your xtc file. It is
> > very unlikely that you will need a .trr file, so you can even set
> nstxout,
> > nstvout and nstfout to zero. Starting your
> > post-processing from a xtc should speed up your analysis process.
> >
> >
> > On another note: Please fill in a subject line in your emails, it makes
> it
> > easier to search and keep track of the
> > ongoing discussions.
> >
> >
> > Best,
> >
> > Christian
> >
> >
> > On 11/7/19 3:12 PM, shakuntala dhurua wrote:
> > > I would like to calculate rmsd of protein system, but there is much
> time
> > > taking for trjcat of all simulated trajectories (.trr file) then
> > generated
> > > .xtc file by using -center -pbc mol flag. from this .xtc file i use to
> > > calculate rms value by using flag g_rms -f .xtc -s .tpr -n .ndx -o
> .xvg I
> > > want to ask here is any other way is available to directly calculate
> rmsd
> > > without using trjcat or less time taking method.
> > --
> > 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-request at gromacs.org.
> >
>
>
> ------------------------------
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> End of gromacs.org_gmx-users Digest, Vol 187, Issue 21
> ******************************************************
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