[gmx-users] Calculate probability of presence of water around a residues
Dear Users, I have two queries 1. I have tried using the select command to Calculate probability of presence of water around a residues by creating an a group in my index analyze.ndx contains a group named ser76 which has the atom position near which i want to find this water (say atom 1313) *gmx select -s md_0_1.tpr -f md_0_1_center.xtc -os no_solv.xvg -select 'name OW and within 0.3 of group ser76' -n analyze.ndx* This command gives an error Error in user input: Selection 'name OW and within 0.3 of group ser76' never matches any atoms. 2. Regarding *MMPBSA calculation* for my protein-ligand simulation. i m using GROMACS 2018 version on the server. What is the procedure for doing the same. Thanks & Regards, Dr. Pooja Kesari Post Doctoral Fellow Department Of Biosciences and Bioengineering Indian Institute of Technology Bombay 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.
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Dear All, I am doing a protein-ligand simulation, when i was try to *add ions to the system* gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr *there was an error* Fatal error: Syntax error - File lig.prm, line 2 Last line read: '[ bondtypes ]' Invalid order for directive bondtypes *my topol.top- ligand defination is as follows * ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include ligand parameters #include "lig.prm" ; Include ligand topology #include "lig.itp" ; Include water topology #include "./charmm36-mar2019.ff/tip3p.itp" I have included the ligand parameter details as suggested in lig.top file generated by cgenff python script. I have attached the itp and prm file for reference. Thanks & Regards, Dr. Pooja Kesari Post Doctoral Fellow Department Of Biosciences and Bioengineering Indian Institute of Technology Bombay 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] gromacs.org_gmx-users Digest, Vol 187, Issue 21
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 OM336VAL O1 1492 -0.63515.9994 ; > qtot -7.365 3329 OM336VAL 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: 1.00 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: 335Protein residues > There are: 1 Other residues > There are: 22473 Water residues > There are: 8Ion 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
[gmx-users] Problem running simulation on gromacs 2018.8 version
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 OM336VAL O1 1492 -0.63515.9994 ; qtot -7.365 3329 OM336VAL 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: 1.00 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: 335Protein residues There are: 1 Other residues There are: 22473 Water residues There are: 8Ion 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. -- 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.
