Re: [gmx-users] peptide ligand
Dear Justin
I performed NVT equilibration for 300 ps , it was done successfully. Yesterday
I wanna do NPT equilibration , so used your npt.mdp file in the GROMACS
tutorial and replaced energgroups and tc-groups by Protein and Protein
water-ions, respectively, specified nstep = 15 , but when I entered,
noticed I had md.log file not npt.log. and it runs to 272000 steps . Why?Would
you please help me how come it runs this way?
From: Justin Lemkul
To: gmx-us...@gromacs.org
Sent: Wednesday, 4 October 2017, 15:19:38
Subject: Re: [gmx-users] peptide ligand
On 10/3/17 1:51 PM, farial tavakoli wrote:
> blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
>#715FFA solid !important; padding-left:1ex !important; background-color:white
>!important; } Because in tuturial , energygroups = protein JZ4So I think ,I
>have to seperate my ligand and Protein in .mdp files and determine H bonds?
>
It has nothing to do with the .mdp file. If you want to analyze hydrogen bonds,
then you can create an .ndx file later for use with gmx hbond.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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Re: [gmx-users] peptide ligand
Dear Justin
Thank you so much for all of your help
best
Farial
From: Justin Lemkul
To: gmx-us...@gromacs.org
Sent: Wednesday, 4 October 2017, 15:19:38
Subject: Re: [gmx-users] peptide ligand
On 10/3/17 1:51 PM, farial tavakoli wrote:
> blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
>#715FFA solid !important; padding-left:1ex !important; background-color:white
>!important; } Because in tuturial , energygroups = protein JZ4So I think ,I
>have to seperate my ligand and Protein in .mdp files and determine H bonds?
>
It has nothing to do with the .mdp file. If you want to analyze hydrogen bonds,
then you can create an .ndx file later for use with gmx hbond.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
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[gmx-users] peptide ligand
Dear GROMACS users I need to run a MD on my Protein-peptide ligand complex in GROMACS. I generated my ligand topology by gromose96 54a7 ff ( [moleculetypes] was Protein_chain_B) and converted it to .itp file to string it in Protein.top file, then, added Protein_chain_B in [ molecules ] directive to create one topology file for my complex. Created newbox and solvate. But when I gave this command:gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr I faced to this error: Group Protein_chain_B referenced in the .mdb file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option of grompp. In spite of , my ligand [ moleculetypes ] in the ligand.itp file is Protein_chain_B , but GROMACS gives error. Would you please advice me how can I solve this problem? Best Farial -- 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] peptide ligand-protein complex topology
Dear GMX users I want to generate a topology for my peptide ligand, but I dont know if I can use "gmx pdb2gmx -f peptide ligand-protein complex.pdb -o peptide ligand-protein complex.gro -water spce -ignh" ?would you please advice me that how can I generate a peptide ligand topology file? I think , it is not needed to use external servers like ATB and I can use pdb2gmx to generate peptide ligand topology. Thanks in advanceFarial -- 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] Doing restart
#yiv4389709560 blockquote, #yiv4389709560 div.yiv4389709560yahoo_quoted
{margin-left:0 !important;border-left:1px #715FFA solid
!important;padding-left:1ex !important;background-color:white;} Dear gmx users
I stoped my md simulation and now i want to restart it.
I use gromacs 2016.3 and issued this command to perform md:Gmx grompp -f
md.mdp -c npt.gro -t npt.cpt -p topol.tpr -n index.ndx -o md_0_1.tprGmx mdrun
-deffnm md_0_1
To restart simulation i issuedGmx mdrun -s md_0_1.tpr -cpi md_0_1.cpt
-appendBut faced to an error:
Fatal error:
File appending requested, but 2 of the 3 output files are not present or are
named differently. For safety reasons, GROMACS-2016 and later only allows file
appending to be used when all files have the same names as they had in the
original run. Checkpointing is merely intended for plain continuation of runs.
For safety reasons you must specify all file names (e.g. with -deffnm), and
all these files must match the names used in the run prior to checkpointing
since we will append to them by default. If the files are not available, you
can add the -noappend flag to mdrun and write separate new parts. For mere
concatenation of files, you should use the gmx trjcat tool instead.
i refered to google but i couldnt understand well what should i type exactly.
would you please help me to restart my md simulation?
Thanks in advanceFarial
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Re: [gmx-users] ligand
Hi Justin Thank you so much with best Farial From: Justin Lemkul To: gmx-us...@gromacs.org Sent: Monday, 14 August 2017, 16:35:58 Subject: Re: [gmx-users] ligand On 8/14/17 2:03 AM, farial tavakoli wrote: > Dear Justin > Thanks for your advice.Now I am trying to create a .gro file from the united > atom pdb structure file obtained from ATB by using :editconf -f xxx.pdb -o > xxx.gro > but faced to this warning: > WARNING: all CONECT records are ignored > would you please advice me how can i solve this problem? You don't. You don't need connectivity information from the PDB because it's all in the topology. This really shouldn't be a "warning," rather an informative note. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] ligand
Dear Justin
Thanks for your advice.Now I am trying to create a .gro file from the united
atom pdb structure file obtained from ATB by using :editconf -f xxx.pdb -o
xxx.gro
but faced to this warning:
WARNING: all CONECT records are ignored
would you please advice me how can i solve this problem?
thanks alotFarial
From: Justin Lemkul
To: gmx-us...@gromacs.org
Sent: Sunday, 13 August 2017, 21:45:53
Subject: Re: [gmx-users] ligand
On 8/13/17 12:29 PM, farial tavakoli wrote:
> blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
>#715FFA solid !important; padding-left:1ex !important; background-color:white
>!important; } Dear justin
> Thank you for your replyI thought that topology file obtained from ATB needs
> to be changed like PRODRG
>
No, they generally should not. ATB is a much better topology source than
PRODRG. That doesn't necessarily mean you should always trust a black box
without some validation, but you shouldn't just blindly go messing with things
because some other program is known to be problematic.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==
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[gmx-users] ligand
Dear GROMACS users I noticed my ligand has some broken bonds and changes in atoms arrengement after md simulation was done. I have read before that no bond is broken and created in simulation . So why have been ligand changed ? I think, i have to notice that when i wanted to create a ligand topology , i used ATB server to create topology and pdb files. and when wanted to reassign the charges and charge groups, noticed that some of the atoms of ligand that have to be in a charge group, were not successive , so decided to rearrange them and replaced them to place them in a charge group. I dont know if it is possible the brocken bonds in the ligand after simulation for 1 ns because of its topology?I am using gromacs 2016.3 and gromos96 54 a7 ff. thanks in advanceTavakoli -- 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] remove the jumps over the boundaries
Dear GROMACS users I am using GROMACS 2016.3 and ran a md simulation on my complex. Now i need to visualize my .xtc file. When i loaded the confout.gro and traj_comp.xtc in VMD , it has pbc problem, so I issued this command: trjconv -s topol.tpr -f traj.xtc -o protein.pdb -pbc nojump -dt 10 but faced to this error: Fatal error: reading tpx file (md_0_1.tpr) version 110 with version 83 program is anybody help me to solve this problem? thanks in advanceFarial -- 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] ATB and PRODRG
Dear gmx users I am using gromos96 54 a7 and gromos 96 a1 force fiels to simulate tow various complexes ( protein + ligand). and used ATB and PRODRG to create topology files for them, respectively. I dont know anything about editing ATB and PRODRG' topology files but reassigingn their charges and charge groups . Is there anything else that I have to do to create a proper topology file for GROMOACS?I would really appreciate for any help. Thanks in advanceFarial -- 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] pdb2gmx
Hello I want to create a .gro and .top file from my protein that contains 379 aminoacids in it's .pdb file by using gromos96 54a7 force field: pdb2gmx -f protein.pdb -o protein.gro -water spce -ignh but when gro and topology files are created , I see that message: Start terminus GLY-12: GLY-NH3+ End terminus PRO-379: COO- Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 368 residues with 3856 atoms Making bonds... Number of bonds was 3938, now 3933 Generating angles, dihedrals and pairs... Before cleaning: 6090 pairs Before cleaning: 8285 dihedrals Making cmap torsions...There are 2746 dihedrals, 2028 impropers, 5756 angles 6090 pairs, 3933 bonds and 0 virtual sites Total mass 42175.307 a.m.u. Total charge -0.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.46# Writing coordinate file... Back Off! I just backed up HDAC2.gro to ./#HDAC2.gro.1# - PLEASE NOTE You have successfully generated a topology from: HDAC2.pdb. The Gromos54a7 force field and the spce water model are used. - ETON ESAELP However, i ignored this message and continued to use grompp gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr but faced to this message: gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.29# Setting the LD random seed to -1863558486 Generated 168 of the 1653 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are: 368 Protein residues There are: 11240 Water residues Analysing Protein... Number of degrees of freedom in T-Coupling group rest is 79005.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.114 0.114 0.114 Estimate for the relative computational load of the PME mesh part: 0.10 This run will generate roughly 3 Mb of data Back Off! I just backed up ions.tpr to ./#ions.tpr.36# Is there anyone to help me? Why pdb2gmx didnt consider all 379 amino acids of my protein and why GOMACS excluded 3 bonded neighours of the protein and SOL?and would you please tell what ' removing all charge groups because cutoff-scheme=Verlet ' means ? I t means the system is neutral ? thanks in advanceFarial -- 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] equilibration
Hi justin Thank you for reply and sorry for sending in another email, because when i wanted to reply, it was rejected.Actually, since i am a new gromacs user, i used all .mdp files ( em.mdp, nvt.mdp,...) in protein-ligand complex ( lysosym 4 ) tuturial in gromacs. And did all the steps and issued all commands that said in this tuturial . I also generated my ligand topology by PRODRG and edited the charges and charge groups . To edit atome charge, according to aminoacids.rtp file, i considered what my atomes are bonded to , in order to best give their charge. Then , regarding to the article : Practical considerations for building GROMOS-compatible small-molecule topologiesEditted the charge groups , but i think , maybe i was wrong in specifying charg groups. In addition, i noticed that there was a wrong bond in the gromacs topology ang gromacs cordinate files, so i corrected them but i dont know if i did right? These are all that i did. I dont know more about generating ligand topology but informatin that said in this tuturial. If you let me, send my ligand topology file to you? With best regardsFarial -- 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] Equilibration
Hi Justin Thank you so much for your reply about minimize ligand in vacuoaccording to :http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System I minimized my protein and ligand alone to fix the problem ( LINCS warning, ( one or more water molecules can not to be settled . check for bad contacts or reduce time step))I checked my protein in desired solvent as i noticed in the previous mail, and it was stable. i minimized my ligand too in vacuo with the .mdp file which you advised me, it was minimized well and monitored by pymol, its configuration was ok. In addition, I reduced the time step from 0,002 to 0.001 , but got the same error in 2 steps.then, reduced the temperature to 100 k , but the same error displayed again. Actually, I cant understand some advices and causes in this site. like: I dont understand some of causes and advices in this site, include:1) you are doing particle insertion in free energy calculations without using soft core2) your position restraints are to coordinates too different from those present in the system3) Make sure the forces don't get that large How can i make sure the forces dont get that large? I dont know what these 3 causes are. I have not recognized where the problem is and fixed it yet. It is wasting my time a lot. My protein and ligand were intact . so what is its problem?would you please help me? and introduce me an appropriate reference to be expert in GROMACS? Thanks in advanceFarial -- 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] ligan minimization in vacuo
Dear gmx-users I have a problem in equilibration my protein-ligand complex and encountered to this error after 2 steps of 5 steps:one or more water molecules can not be settled. check for bad contacts or reduce the time steps. so I decided to create a topology for my designed drug (50 atoms) as a ligand to minimize it in the vacuo in the absence of the protein to check if it minimizes , so i tried to change the .itp file obtained from PRODRG to create a .top file, in this way:I added " ; Include forcefield parameters #include "gromos43a1.ff/forcefield.itp " above the [ moleculetype ] directive as a first line , then added [ system ] and [ molecule ] directives under the ligand, respectively : 23 24 26 27 1 180.0 33.5 2 180.0 33.5 2 ; dih CAS CAR NAQ CAN 32 27 26 24 1 180.0 33.5 2 180.0 33.5 2 ; dih CAM CAN NAQ CAR 39 37 36 30 1 180.0 5.9 2 180.0 5.9 2 ; dih SAG CAH CAK CAP 40 48 49 50 1 180.0 7.1 2 180.0 7.1 2 ; dih CAA CAF OAJ HAJ ; Ligand position restraints #ifdef POSRES #include "posre_DRG.itp" #endif ; Include water topology #include "gromos43a1.ff/spc.itp" [ system ] ; Name DRG in water [ molecules ] ; Compound #mols DRG 1 issued this command:gmx grompp -v -f em.mdp -c DRG.gro -p DRG.top -o DRG-EM-vacuum.tprgmx mdrun -v -deffnm DRG-EM-vacuum -c DRG-EM-vacuum.gro and simulation results: Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps = 5 Step= 0, Dmax= 1.0e-02 nm, Epot= 1.41636e+03 Fmax= 2.81150e+04, atom= 25 Step= 1, Dmax= 1.0e-02 nm, Epot= 1.01416e+03 Fmax= 1.21118e+04, atom= 25 Step= 2, Dmax= 1.2e-02 nm, Epot= 7.87016e+02 Fmax= 4.71639e+03, atom= 25 Step= 3, Dmax= 1.4e-02 nm, Epot= 6.94638e+02 Fmax= 5.88719e+03, atom= 15 Step= 5, Dmax= 8.6e-03 nm, Epot= 6.79808e+02 Fmax= 7.13390e+03, atom= 15 Step= 7, Dmax= 5.2e-03 nm, Epot= 6.29169e+02 Fmax= 1.31714e+03, atom= 25 Step= 8, Dmax= 6.2e-03 nm, Epot= 6.12279e+02 Fmax= 2.91712e+03, atom= 14 Step= 10, Dmax= 3.7e-03 nm, Epot= 6.04849e+02 Fmax= 2.77294e+03, atom= 27 Step= 12, Dmax= 2.2e-03 nm, Epot= 5.86062e+02 Fmax= 9.77798e+02, atom= 24 writing lowest energy coordinates. Back Off! I just backed up DRG-EM-vacuum.gro to ./#DRG-EM-vacuum.gro.1# Steepest Descents converged to Fmax < 1000 in 13 steps Potential Energy = 5.8606232e+02 Maximum force = 9.7779791e+02 on atom 24 Norm of force = 3.8248090e+02 Simulation ended prematurely, no performance report will be written. here's my em.mdp file: integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform energygrps = system ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; long range electrostatic cut-off rvdw = 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions I just wanted to know if I did correct?In addition after minimization in vacuo , checked my ligand in pymol and noticed it is disintegrated. Is there anyone help me how come it is disintegrated ,however i edited the .itp file obtained from PRODRG ( charges and charg groups)? How can i fix this problem to equilibrate my complex? thank you in advance Farial -- 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] how to creat ligand topology to minimize in vacuo in the absence of the protein
Dear gmx-usersI need to create a topology for my designed drug as a ligand to minimize it in the vacuo in the absence of the protein. But I dont know how can i convert the DRG.itp file which I obtained from PRODRG site to a .top file . I searched in the Google and found " Re: minimizing ligand only "but couldnt find a clear explanation for that.Could anyone advice me to fix this problem? sorry if the request seems to be trivial. but i really cant understand what to do. Thanks in advance Farial -- 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] EQUILIBRATION
HiI am a new GROMACS user and trying to run md on HDAC2 with PDB ID: 4LY1. but when I wanted to performance equilibration , i got this ERROR: step 1: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate Would you please help me to fix this problem? These are all stages which I did: I took 4LY1.pdb file from PDB site and removed B and C chains and all ligands and water molecules from it and left just chain A and HETATM ZN A . I constructed my protein topology by using gromos 43a1 and this command:pdb2gmx -f 4LY1.pdb -o 4LY1.gro -water spc then made a complex.gro file which include 4LY1.gro and DRG.gro which i got from PRODRG site. I also copy paste ; Include ligand topology #include "DRG.itp" in the topology file and added DRG as a ligand in [ molecules ] directive. Then I defined box by using this command : gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0 then defined solvate by : gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro then used grommp to assemble a .tpr file by using a .mdp file and this command : gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr that was my .mdp afile : integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform energygrps = system; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions and added 2 CL ions since my total charge was 2.00 because of zn ion. gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 2 then for minimization, i replaced energygroups from system to protein DRG in em_real.mdp. that was my em_real.mdp file: integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force < 10.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform energygrps = protein DRG ; Which energy group(s) to write to disk ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.0 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.0 ; long range electrostatic cut-off rvdw= 1.0 ; long range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions and typed these command: gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tprand gmx mdrun -v -deffnm em GROMACS replies: Steepest Descents converged to Fmax < 1000 in 1833 steps Potential Energy = -5.6356275e+05 Maximum force = 9.7815100e+02 on atom 3452 Norm of force = 3.1465845e+01 Simulation ended prematurely, no performance report will be written. Is there any problem that simulation ended prematurely? Then for equilibriation i typed gmx genrestr -f jz4.gro -o posre_jz4.itp -fc 1000 1000 1000 and in order to restrain both the protein and the ligand simultaneously, I specify define = -DPOSRES -DPOSRES_LIG in the .mdp file. then typed gmx make_ndx -f em.gro -o index.ndx to merge the protein and DRG. and selected protein and DRG by : > 1 | 14 > qthen set tc_grps = Protein_DRG Water_and_ions in NVT.mdp file to achieve my > desired "Protein Non-Protein" effect. that was my NVT.mdp file: title = Protein-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand integrator = md ; leap-frog integratornsteps = 5 ; 2 * 5 = 100 psdt
