Re: [gmx-users] parameters problem
On 3/11/14, 6:32 AM, Nidhi Katyal wrote: Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well as [molecule] entry. I have followed the following procedure to #include while creating my first molecule: Run pdb2gmx command. Added #include "ligand.itp" after #include "charmm27.ff/forcefield.itp" but before [ moleculetype ] ; Namenrexcl Protein_chain_A 3 and added at the end: [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 1 SOL 17063 then I have merged protein and ligand coordinates by inserting ATOM lines from ligand.pdb to *.pdb generated after pdb2gmx command. Then. I run editconf, genbox and finally grompp command. After which I got following error: Fatal error: No such moleculetype LIG My both *.itp and *.pdb files contains LIG. How to rectify the error? Thanks in advance. Residue name and [moleculetype] name are not necessarily equivalent. You'll have to post the actual content of lig.itp to get any real useful diagnostic feedback. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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 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] parameters problem
Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well as [molecule] entry. I have followed the following procedure to #include while creating my first molecule: Run pdb2gmx command. Added #include "ligand.itp" after #include "charmm27.ff/forcefield.itp" but before [ moleculetype ] ; Namenrexcl Protein_chain_A 3 and added at the end: [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 1 SOL 17063 then I have merged protein and ligand coordinates by inserting ATOM lines from ligand.pdb to *.pdb generated after pdb2gmx command. Then. I run editconf, genbox and finally grompp command. After which I got following error: Fatal error: No such moleculetype LIG My both *.itp and *.pdb files contains LIG. How to rectify the error? Thanks in advance. On Tue, Mar 11, 2014 at 1:39 AM, Mark Abraham wrote: > Probably you will see that your ligand.itp has an [atomtypes] entry as well > as a [molecule] entry, and the former cannot follow any instance of the > latter. Such an .itp file must be #included to create the first molecule. > You have your protein [molecule] above the #include "ligand.itp" at the > moment, which would cause this problem. > > Mark > > > On Mon, Mar 10, 2014 at 7:09 PM, Nidhi Katyal >wrote: > > > To test swiss param parameters, I have generated *.pdb and *.itp files > from > > it. In the genbox command, I have used -ci *.pdb -nmol 2. > > I have included *.itp in the topology as: > > > > ; Include Position restraint file > > ;#ifdef POSRES > > ;#include "posre.itp" > > ;#endif > > > > ;Include ligand topology > > #include "ligand.itp" > > > > ; Include water topology > > #include "charmm27.ff/tip3p.itp" > > > > #ifdef POSRES_WATER > > ; Position restraint for each water oxygen > > [ position_restraints ] > > ; i funct fcxfcyfcz > >11 1000 1000 1000 > > #endif > > > > ; Include topology for ions > > #include "charmm27.ff/ions.itp" > > > > [ system ] > > ; Name > > Protein in water > > > > [ molecules ] > > ; Compound#mols > > Protein_chain_A 1 > > LIG 2 > > SOL 12904 > > > > But after I run grompp command, I get following error: > > > > Fatal error: > > Syntax error - File ligand.itp, line 7 > > Last line read: > > '[ atomtypes ] ' > > Invalid order for directive atomtypes > > > > Please help me rectify the problem of the order getting violated although > > same worked for topology generated by PRODRG. > > > > Thanks in advance. > > > > > > > > On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul wrote: > > > > > > > > > > > On 3/10/14, 8:21 AM, Nidhi Katyal wrote: > > > > > >> Thanks Justin. I would also like to know the reliability of parameters > > >> generated using swiss param. > > >> > > >> > > >> > > > I have no personal experience with it. My rule is to never trust > > anything > > > from a black-box server without verifying it and assessing any > > information > > > about penalties, deviations, etc. that it provides. > > > > > > -Justin > > > > > > > > > On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul > wrote: > > >> > > >> > > >>> > > >>> On 3/10/14, 2:45 AM, Nidhi Katyal wrote: > > >>> > > >>> Thank you Mark and Justin. > > Now, I have carried out simulations using PME electrostatics and > using > > all other > > parameters (except gromos 96 43a1 ff used) as suggested in > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > gmx-tutorials/lysozyme/ > > > > The protein is not loosing its structure now. But the problem is if > I > > carry out > > simulations in the presence of experimentally known stabiliser > > generated > > using > > ProDrg (keeping all the parameters same while simulating both in the > > presence > > and absence of stabiliser), the partial loss of secondary structure > is > > observed > > in the presence of stabilizer relative to the case in its absence at > > 350K > > thereby implying simulations going against experimental observations > > (although > > slight stabilization was observed at 300K). Simulations were > repeated > > twice with > > two different force fields. > > However if I use above em,pr,full parameters with cut-off > > electrostatics, > > although secondary structure is lost in the initial stages but I > could > > clearly > > see the stabilization behaviour of additive in terms of secondary > > structure > > retainment till longer time. Is this observation a matter of chance- > > reliable or > > not? What could be the possible reason for not observing such > > stabilization with > > better parameters? > > > > > > Cutoff electrostatics are horribly inaccurate. The fact that you > > >>> conveniently see what you hope to when using a plain cutoff is likely > > by > > >>> chance. > > >>> > > >>> The bigger
Re: [gmx-users] parameters problem
Probably you will see that your ligand.itp has an [atomtypes] entry as well as a [molecule] entry, and the former cannot follow any instance of the latter. Such an .itp file must be #included to create the first molecule. You have your protein [molecule] above the #include "ligand.itp" at the moment, which would cause this problem. Mark On Mon, Mar 10, 2014 at 7:09 PM, Nidhi Katyal wrote: > To test swiss param parameters, I have generated *.pdb and *.itp files from > it. In the genbox command, I have used -ci *.pdb -nmol 2. > I have included *.itp in the topology as: > > ; Include Position restraint file > ;#ifdef POSRES > ;#include "posre.itp" > ;#endif > > ;Include ligand topology > #include "ligand.itp" > > ; Include water topology > #include "charmm27.ff/tip3p.itp" > > #ifdef POSRES_WATER > ; Position restraint for each water oxygen > [ position_restraints ] > ; i funct fcxfcyfcz >11 1000 1000 1000 > #endif > > ; Include topology for ions > #include "charmm27.ff/ions.itp" > > [ system ] > ; Name > Protein in water > > [ molecules ] > ; Compound#mols > Protein_chain_A 1 > LIG 2 > SOL 12904 > > But after I run grompp command, I get following error: > > Fatal error: > Syntax error - File ligand.itp, line 7 > Last line read: > '[ atomtypes ] ' > Invalid order for directive atomtypes > > Please help me rectify the problem of the order getting violated although > same worked for topology generated by PRODRG. > > Thanks in advance. > > > > On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul wrote: > > > > > > > On 3/10/14, 8:21 AM, Nidhi Katyal wrote: > > > >> Thanks Justin. I would also like to know the reliability of parameters > >> generated using swiss param. > >> > >> > >> > > I have no personal experience with it. My rule is to never trust > anything > > from a black-box server without verifying it and assessing any > information > > about penalties, deviations, etc. that it provides. > > > > -Justin > > > > > > On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul wrote: > >> > >> > >>> > >>> On 3/10/14, 2:45 AM, Nidhi Katyal wrote: > >>> > >>> Thank you Mark and Justin. > Now, I have carried out simulations using PME electrostatics and using > all other > parameters (except gromos 96 43a1 ff used) as suggested in > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > gmx-tutorials/lysozyme/ > > The protein is not loosing its structure now. But the problem is if I > carry out > simulations in the presence of experimentally known stabiliser > generated > using > ProDrg (keeping all the parameters same while simulating both in the > presence > and absence of stabiliser), the partial loss of secondary structure is > observed > in the presence of stabilizer relative to the case in its absence at > 350K > thereby implying simulations going against experimental observations > (although > slight stabilization was observed at 300K). Simulations were repeated > twice with > two different force fields. > However if I use above em,pr,full parameters with cut-off > electrostatics, > although secondary structure is lost in the initial stages but I could > clearly > see the stabilization behaviour of additive in terms of secondary > structure > retainment till longer time. Is this observation a matter of chance- > reliable or > not? What could be the possible reason for not observing such > stabilization with > better parameters? > > > Cutoff electrostatics are horribly inaccurate. The fact that you > >>> conveniently see what you hope to when using a plain cutoff is likely > by > >>> chance. > >>> > >>> The bigger issue is the use of PRODRG parameters. As I have said > >>> numerous > >>> times on this list, the parameters it produces are demonstrably > >>> inaccurate > >>> and require reparametrization. > >>> > >>> http://pubs.acs.org/doi/abs/10.1021/ci100335w > >>> > >>> > >>> -Justin > >>> > >>> -- > >>> == > >>> > >>> Justin A. Lemkul, Ph.D. > >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow > >>> > >>> Department of Pharmaceutical Sciences > >>> School of Pharmacy > >>> Health Sciences Facility II, Room 601 > >>> 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 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/gr
Re: [gmx-users] parameters problem
To test swiss param parameters, I have generated *.pdb and *.itp files from it. In the genbox command, I have used -ci *.pdb -nmol 2. I have included *.itp in the topology as: ; Include Position restraint file ;#ifdef POSRES ;#include "posre.itp" ;#endif ;Include ligand topology #include "ligand.itp" ; Include water topology #include "charmm27.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "charmm27.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 LIG 2 SOL 12904 But after I run grompp command, I get following error: Fatal error: Syntax error - File ligand.itp, line 7 Last line read: '[ atomtypes ] ' Invalid order for directive atomtypes Please help me rectify the problem of the order getting violated although same worked for topology generated by PRODRG. Thanks in advance. On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul wrote: > > > On 3/10/14, 8:21 AM, Nidhi Katyal wrote: > >> Thanks Justin. I would also like to know the reliability of parameters >> generated using swiss param. >> >> >> > I have no personal experience with it. My rule is to never trust anything > from a black-box server without verifying it and assessing any information > about penalties, deviations, etc. that it provides. > > -Justin > > > On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul wrote: >> >> >>> >>> On 3/10/14, 2:45 AM, Nidhi Katyal wrote: >>> >>> Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/lysozyme/ The protein is not loosing its structure now. But the problem is if I carry out simulations in the presence of experimentally known stabiliser generated using ProDrg (keeping all the parameters same while simulating both in the presence and absence of stabiliser), the partial loss of secondary structure is observed in the presence of stabilizer relative to the case in its absence at 350K thereby implying simulations going against experimental observations (although slight stabilization was observed at 300K). Simulations were repeated twice with two different force fields. However if I use above em,pr,full parameters with cut-off electrostatics, although secondary structure is lost in the initial stages but I could clearly see the stabilization behaviour of additive in terms of secondary structure retainment till longer time. Is this observation a matter of chance- reliable or not? What could be the possible reason for not observing such stabilization with better parameters? Cutoff electrostatics are horribly inaccurate. The fact that you >>> conveniently see what you hope to when using a plain cutoff is likely by >>> chance. >>> >>> The bigger issue is the use of PRODRG parameters. As I have said >>> numerous >>> times on this list, the parameters it produces are demonstrably >>> inaccurate >>> and require reparametrization. >>> >>> http://pubs.acs.org/doi/abs/10.1021/ci100335w >>> >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> 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 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. >>> >>> > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > 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 http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! >
Re: [gmx-users] parameters problem
On 3/10/14, 8:21 AM, Nidhi Katyal wrote: Thanks Justin. I would also like to know the reliability of parameters generated using swiss param. I have no personal experience with it. My rule is to never trust anything from a black-box server without verifying it and assessing any information about penalties, deviations, etc. that it provides. -Justin On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul wrote: On 3/10/14, 2:45 AM, Nidhi Katyal wrote: Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ gmx-tutorials/lysozyme/ The protein is not loosing its structure now. But the problem is if I carry out simulations in the presence of experimentally known stabiliser generated using ProDrg (keeping all the parameters same while simulating both in the presence and absence of stabiliser), the partial loss of secondary structure is observed in the presence of stabilizer relative to the case in its absence at 350K thereby implying simulations going against experimental observations (although slight stabilization was observed at 300K). Simulations were repeated twice with two different force fields. However if I use above em,pr,full parameters with cut-off electrostatics, although secondary structure is lost in the initial stages but I could clearly see the stabilization behaviour of additive in terms of secondary structure retainment till longer time. Is this observation a matter of chance- reliable or not? What could be the possible reason for not observing such stabilization with better parameters? Cutoff electrostatics are horribly inaccurate. The fact that you conveniently see what you hope to when using a plain cutoff is likely by chance. The bigger issue is the use of PRODRG parameters. As I have said numerous times on this list, the parameters it produces are demonstrably inaccurate and require reparametrization. http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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 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] parameters problem
Thanks Justin. I would also like to know the reliability of parameters generated using swiss param. On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul wrote: > > > On 3/10/14, 2:45 AM, Nidhi Katyal wrote: > >> Thank you Mark and Justin. >> Now, I have carried out simulations using PME electrostatics and using >> all other >> parameters (except gromos 96 43a1 ff used) as suggested in >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ >> gmx-tutorials/lysozyme/ >> >> The protein is not loosing its structure now. But the problem is if I >> carry out >> simulations in the presence of experimentally known stabiliser generated >> using >> ProDrg (keeping all the parameters same while simulating both in the >> presence >> and absence of stabiliser), the partial loss of secondary structure is >> observed >> in the presence of stabilizer relative to the case in its absence at 350K >> thereby implying simulations going against experimental observations >> (although >> slight stabilization was observed at 300K). Simulations were repeated >> twice with >> two different force fields. >> However if I use above em,pr,full parameters with cut-off electrostatics, >> although secondary structure is lost in the initial stages but I could >> clearly >> see the stabilization behaviour of additive in terms of secondary >> structure >> retainment till longer time. Is this observation a matter of chance- >> reliable or >> not? What could be the possible reason for not observing such >> stabilization with >> better parameters? >> >> > Cutoff electrostatics are horribly inaccurate. The fact that you > conveniently see what you hope to when using a plain cutoff is likely by > chance. > > The bigger issue is the use of PRODRG parameters. As I have said numerous > times on this list, the parameters it produces are demonstrably inaccurate > and require reparametrization. > > http://pubs.acs.org/doi/abs/10.1021/ci100335w > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > 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 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] parameters problem
On 3/10/14, 2:45 AM, Nidhi Katyal wrote: Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ The protein is not loosing its structure now. But the problem is if I carry out simulations in the presence of experimentally known stabiliser generated using ProDrg (keeping all the parameters same while simulating both in the presence and absence of stabiliser), the partial loss of secondary structure is observed in the presence of stabilizer relative to the case in its absence at 350K thereby implying simulations going against experimental observations (although slight stabilization was observed at 300K). Simulations were repeated twice with two different force fields. However if I use above em,pr,full parameters with cut-off electrostatics, although secondary structure is lost in the initial stages but I could clearly see the stabilization behaviour of additive in terms of secondary structure retainment till longer time. Is this observation a matter of chance- reliable or not? What could be the possible reason for not observing such stabilization with better parameters? Cutoff electrostatics are horribly inaccurate. The fact that you conveniently see what you hope to when using a plain cutoff is likely by chance. The bigger issue is the use of PRODRG parameters. As I have said numerous times on this list, the parameters it produces are demonstrably inaccurate and require reparametrization. http://pubs.acs.org/doi/abs/10.1021/ci100335w -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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 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] parameters problem
Thank you Mark and Justin. Now, I have carried out simulations using PME electrostatics and using all other parameters (except gromos 96 43a1 ff used) as suggested in http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/ The protein is not loosing its structure now. But the problem is if I carry out simulations in the presence of experimentally known stabiliser generated using ProDrg (keeping all the parameters same while simulating both in the presence and absence of stabiliser), the partial loss of secondary structure is observed in the presence of stabilizer relative to the case in its absence at 350K thereby implying simulations going against experimental observations (although slight stabilization was observed at 300K). Simulations were repeated twice with two different force fields. However if I use above em,pr,full parameters with cut-off electrostatics, although secondary structure is lost in the initial stages but I could clearly see the stabilization behaviour of additive in terms of secondary structure retainment till longer time. Is this observation a matter of chance- reliable or not? What could be the possible reason for not observing such stabilization with better parameters? Looking forward to your reply.Thanks in advance. Nidhi On Mon, Feb 17, 2014 at 7:12 PM, Justin Lemkul wrote: > > > On 2/17/14, 4:16 AM, Nidhi Katyal wrote: > >> Dear all >> >> I am trying to simulate a protein in 3 steps: energy minimization (using >> em.mdp), position restraints (using pr.mdp) and final production run by >> NPT >> ensemble (using full.mdp) at 300K >> >> At this temperature, it is known by previous literature survey that >> protein >> keeps its secondary structure almost intact. But according to my >> simulations (done thrice), protein starts loosing its secondary structure >> around 6-8ns only. I have used the following parameters: >> >> *em.mdp* >> >> ; >> ; User spoel (236) >> >> ; Wed Nov 3 17:12:44 1993 >> ; Input file >> ; >> cpp = /usr/bin/cpp >> define = -DFLEX_SPC >> constraints = none >> integrator = steep >> nsteps = 25 >> ; >> ; Energy minimizing stuff >> ; >> emtol = 2000 >> emstep = 0.001 >> >> nstcomm = 1 >> ns_type = grid >> rlist = 1 >> rcoulomb= 1.0 >> rvdw= 1.0 >> Tcoupl = no >> Pcoupl = no >> gen_vel = no >> >> >> *pr.mdp* >> >> ; >> ; User spoel (236) >> >> ; Wed Nov 3 17:12:44 1993 >> ; Input file >> ; >> title = Yo >> cpp = /usr/bin/cpp >> define = -DPOSRES >> constraints = all-bonds >> integrator = md >> dt = 0.002 ; ps ! >> nsteps = 5 ; total 100 ps. >> nstcomm = 1 >> nstxout = 5000 >> nstvout = 5000 >> nstfout = 0 >> nstlog = 10 >> nstenergy = 10 >> nstlist = 10 >> ns_type = grid >> rlist = 1.0 >> rcoulomb= 1.0 >> rvdw= 1.0 >> ; Berendsen temperature coupling is on in two groups >> Tcoupl = berendsen >> tc-grps = ProteinNon-protein >> tau_t = 0.10.1 >> ref_t = 300300 >> ; Energy monitoring >> energygrps = ProteinNon-protein >> ; Pressure coupling is not on >> Pcoupl = no >> tau_p = 0.5 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> ; Generate velocites is on at 300 K. >> gen_vel = yes >> gen_temp= 300.0 >> gen_seed= 173529 >> >> >> *full.mdp* >> >> ; >> ; User spoel (236) >> >> ; Wed Nov 3 17:12:44 1993 >> ; Input file >> ; >> title = Yo >> cpp = /usr/bin/cpp >> constraints = all-bonds >> integrator = md >> dt = 0.002 ; ps ! >> nsteps = 2500 ; total 5 ps. >> nstcomm = 1 >> nstxout = 5000 >> nstvout = 5000 >> nstfout = 0 >> nstlog = 5000 >> nstenergy = 5000 >> nstlist = 10 >> ns_type = grid >> rlist = 1.0 >> rcoulomb= 1.0 >> rvdw= 1.0 >> ; Berendsen temperature coupling is on in two groups >> Tcoupl = berendsen >> tc-grps = Protein Non-protein >> tau_t = 0.10.1 >> ref_t = 300 300 >> ; Energy monitoring >> energygrps = Protein Non-protein >> ; Isotropic pressure coupling is now on >> Pcoupl = berendsen >> Pcoupltype = isotropic >> tau_p = 0.5 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> ; Generate velocites is off
Re: [gmx-users] parameters problem
On 2/17/14, 4:16 AM, Nidhi Katyal wrote: Dear all I am trying to simulate a protein in 3 steps: energy minimization (using em.mdp), position restraints (using pr.mdp) and final production run by NPT ensemble (using full.mdp) at 300K At this temperature, it is known by previous literature survey that protein keeps its secondary structure almost intact. But according to my simulations (done thrice), protein starts loosing its secondary structure around 6-8ns only. I have used the following parameters: *em.mdp* ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 25 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.001 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no *pr.mdp* ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5 ; total 100 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = ProteinNon-protein tau_t = 0.10.1 ref_t = 300300 ; Energy monitoring energygrps = ProteinNon-protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 *full.mdp* ; ; User spoel (236) ; Wed Nov 3 17:12:44 1993 ; Input file ; title = Yo cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 2500 ; total 5 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.10.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 300 K. gen_vel = no gen_temp= 300.0 gen_seed= 173529 I don't think it is the problem of thermostat because even after using V-rescale for temperature coupling and Parinello Rahman for pressure coupling, my protein loses its secondary structure in the initial time of simulation. Also, I have carried out various checks (like potential energy convergence after em, temperature check after pr, and pressure and density check after full), all of which seems to converge well. Please help me figure out the problem. The more relevant information is which force field you are using. It is also possible that the introduction of pressure coupling without restraints can cause screwy behavior, so a restrained NPT equilibration is probably worthwhile, as well. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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 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] parameters problem
Seems like you're using cut-off electrostatics, which would be a good way of picking lottery numbers, and that's about all. Mark On Mon, Feb 17, 2014 at 10:16 AM, Nidhi Katyal wrote: > Dear all > > I am trying to simulate a protein in 3 steps: energy minimization (using > em.mdp), position restraints (using pr.mdp) and final production run by NPT > ensemble (using full.mdp) at 300K > > At this temperature, it is known by previous literature survey that protein > keeps its secondary structure almost intact. But according to my > simulations (done thrice), protein starts loosing its secondary structure > around 6-8ns only. I have used the following parameters: > > *em.mdp* > > ; > ; User spoel (236) > ; Wed Nov 3 17:12:44 1993 > ; Input file > ; > cpp = /usr/bin/cpp > define = -DFLEX_SPC > constraints = none > integrator = steep > nsteps = 25 > ; > ; Energy minimizing stuff > ; > emtol = 2000 > emstep = 0.001 > > nstcomm = 1 > ns_type = grid > rlist = 1 > rcoulomb= 1.0 > rvdw= 1.0 > Tcoupl = no > Pcoupl = no > gen_vel = no > > > *pr.mdp* > > ; > ; User spoel (236) > ; Wed Nov 3 17:12:44 1993 > ; Input file > ; > title = Yo > cpp = /usr/bin/cpp > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 5 ; total 100 ps. > nstcomm = 1 > nstxout = 5000 > nstvout = 5000 > nstfout = 0 > nstlog = 10 > nstenergy = 10 > nstlist = 10 > ns_type = grid > rlist = 1.0 > rcoulomb= 1.0 > rvdw= 1.0 > ; Berendsen temperature coupling is on in two groups > Tcoupl = berendsen > tc-grps = ProteinNon-protein > tau_t = 0.10.1 > ref_t = 300300 > ; Energy monitoring > energygrps = ProteinNon-protein > ; Pressure coupling is not on > Pcoupl = no > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp= 300.0 > gen_seed= 173529 > > > *full.mdp* > > ; > ; User spoel (236) > ; Wed Nov 3 17:12:44 1993 > ; Input file > ; > title = Yo > cpp = /usr/bin/cpp > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 2500 ; total 5 ps. > nstcomm = 1 > nstxout = 5000 > nstvout = 5000 > nstfout = 0 > nstlog = 5000 > nstenergy = 5000 > nstlist = 10 > ns_type = grid > rlist = 1.0 > rcoulomb= 1.0 > rvdw= 1.0 > ; Berendsen temperature coupling is on in two groups > Tcoupl = berendsen > tc-grps = Protein Non-protein > tau_t = 0.10.1 > ref_t = 300 300 > ; Energy monitoring > energygrps = Protein Non-protein > ; Isotropic pressure coupling is now on > Pcoupl = berendsen > Pcoupltype = isotropic > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > ; Generate velocites is off at 300 K. > gen_vel = no > gen_temp= 300.0 > gen_seed= 173529 > > I don't think it is the problem of thermostat because even after using > V-rescale for temperature coupling and Parinello Rahman for pressure > coupling, my protein loses its secondary structure in the initial time of > simulation. > > Also, I have carried out various checks (like potential energy convergence > after em, temperature check after pr, and pressure and density check after > full), all of which seems to converge well. > > Please help me figure out the problem. > -- > 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.
