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-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > 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 <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Regarding multiple ligands' topology > Message-ID: <7fda6310-d8d4-2a53-c42f-9d700c3f6...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 2 > Date: Fri, 8 Nov 2019 18:06:35 +0530 > From: pooja kesari <poojakesar...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Problem running simulation on gromacs 2018.8 > version > Message-ID: > < > cahxjgagqdqj2x0-mqazax7zmjgmrnqpnhotkn+8xszdybjn...@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 <b...@kth.se> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] gmx trjorder > Message-ID: <9f734a77-33b7-449e-cebf-84983b205...@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 <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Problem running simulation on gromacs 2018.8 > version > Message-ID: <53533d16-c602-07a4-33ba-5f36554b6...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 5 > Date: Fri, 8 Nov 2019 15:00:54 +0100 > From: Christian Blau <b...@kth.se> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] (no subject) > Message-ID: <37964cff-5b95-0e43-5274-1e04e9c30...@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.dhuru...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] (no subject) > Message-ID: > < > cafxbq7f-pamwewgzmebhcacy8wjw+-krb-icpb-zimek5yb...@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, <b...@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-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. > > End of gromacs.org_gmx-users Digest, Vol 187, Issue 21 > ****************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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