Re: [gmx-users] Extra number of bonds created than specified (ZN-CYS)
Hi, You seem to be suggesting that there is an entry in [bonds] that is 4800 to 3368, and three others from that cysteine residue. That's highly surprising, because this kind of workflow seems like something people should have tried before... If so, then it would be good to file a report at http://redmine.gromacs.org with your Gromacs version, input files and pdb2gmx call, so that we can reproduce it and fix it. You can of course delete the lines with the spurious [bonds] entry. grompp might complain if there are [angles] or [dihedrals] related to those, which you could also delete. You should verify that the final bonds+angles+dihedrals in the topology are what you think they should be. Mark On Fri, Nov 14, 2014 at 8:03 AM, Nixon Raj nixn...@gmail.com wrote: Im dealing a protein with 4799 atoms and 1 ZN ion totally 4800 atoms. I need to form bonds between 4CYS-ZN , where i have equilibrium bond length, force constant and partial charges for the same fixed. Since i have new partial charge for Zn ion , i have created an ZN ion in name ZN1 . My specbond.dat is modified accordingly to add the necessary bonds , CYZ SG 1 ZN1 ZN 1 0.23CYZ ZN1 Running the pdb2gmx yielded me Linking CYZ-210 SG-3368 and ZN1-299 ZN1-4800... Linking CYZ-260 SG-4195 and ZN1-299 ZN1-4800... Linking CYZ-263 SG-4250 and ZN1-299 ZN1-4800... Linking CYZ-270 SG-4358 and ZN1-299 ZN1-4800... Start terminus MET-1: NH3+ End terminus TYR-298: COO- Opening force field file ./charmm36.ff/merged.arn Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 299 residues with 4800 atoms Making bonds... Number of bonds was 4859, now 4859 Generating angles, dihedrals and pairs... Before cleaning: 12729 pairs Before cleaning: 12834 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 296 cmap torsion pairs There are 12834 dihedrals, 838 impropers, 8752 angles 12621 pairs, 4859 bonds and 0 virtual sites Total mass 34700.069 a.m.u. Total charge -8.000 e Writing topology But i could find 12 extra bonds created with ZN1(4800) in my topology file. But the dihedrals and angles are in correct numbers. Each residue sharing 4 bonds with ZN1 (4800), i.e) CA-ZN1, HB1-ZN1, HB2-ZN1 and SG-ZN1 , where i need only one bond i.e) SG-ZN1 with each cystein residue. Please help me to cross this roadblock. -- 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] Extra number of bonds created than specified (ZN-CYS)
Hi Mark Yeah i deleted it manually from the topology file and could able to progress further. But how could this happen. So its better to file a report as you suggested. Thanks On Fri, Nov 14, 2014 at 4:50 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You seem to be suggesting that there is an entry in [bonds] that is 4800 to 3368, and three others from that cysteine residue. That's highly surprising, because this kind of workflow seems like something people should have tried before... If so, then it would be good to file a report at http://redmine.gromacs.org with your Gromacs version, input files and pdb2gmx call, so that we can reproduce it and fix it. You can of course delete the lines with the spurious [bonds] entry. grompp might complain if there are [angles] or [dihedrals] related to those, which you could also delete. You should verify that the final bonds+angles+dihedrals in the topology are what you think they should be. Mark On Fri, Nov 14, 2014 at 8:03 AM, Nixon Raj nixn...@gmail.com wrote: Im dealing a protein with 4799 atoms and 1 ZN ion totally 4800 atoms. I need to form bonds between 4CYS-ZN , where i have equilibrium bond length, force constant and partial charges for the same fixed. Since i have new partial charge for Zn ion , i have created an ZN ion in name ZN1 . My specbond.dat is modified accordingly to add the necessary bonds , CYZ SG 1 ZN1 ZN 1 0.23CYZ ZN1 Running the pdb2gmx yielded me Linking CYZ-210 SG-3368 and ZN1-299 ZN1-4800... Linking CYZ-260 SG-4195 and ZN1-299 ZN1-4800... Linking CYZ-263 SG-4250 and ZN1-299 ZN1-4800... Linking CYZ-270 SG-4358 and ZN1-299 ZN1-4800... Start terminus MET-1: NH3+ End terminus TYR-298: COO- Opening force field file ./charmm36.ff/merged.arn Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 299 residues with 4800 atoms Making bonds... Number of bonds was 4859, now 4859 Generating angles, dihedrals and pairs... Before cleaning: 12729 pairs Before cleaning: 12834 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 296 cmap torsion pairs There are 12834 dihedrals, 838 impropers, 8752 angles 12621 pairs, 4859 bonds and 0 virtual sites Total mass 34700.069 a.m.u. Total charge -8.000 e Writing topology But i could find 12 extra bonds created with ZN1(4800) in my topology file. But the dihedrals and angles are in correct numbers. Each residue sharing 4 bonds with ZN1 (4800), i.e) CA-ZN1, HB1-ZN1, HB2-ZN1 and SG-ZN1 , where i need only one bond i.e) SG-ZN1 with each cystein residue. Please help me to cross this roadblock. -- 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. -- 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] Extra number of bonds created than specified (ZN-CYS)
On Fri, Nov 14, 2014 at 9:58 AM, Nixon Raj nixn...@gmail.com wrote: Hi Mark Yeah i deleted it manually from the topology file and could able to progress further. But how could this happen. You really don't want to know ;-) So its better to file a report as you suggested. Thanks Please do. That code is nearly impossible to reason about, so the actual problem case is likely to be critical for fixing it. Mark On Fri, Nov 14, 2014 at 4:50 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, You seem to be suggesting that there is an entry in [bonds] that is 4800 to 3368, and three others from that cysteine residue. That's highly surprising, because this kind of workflow seems like something people should have tried before... If so, then it would be good to file a report at http://redmine.gromacs.org with your Gromacs version, input files and pdb2gmx call, so that we can reproduce it and fix it. You can of course delete the lines with the spurious [bonds] entry. grompp might complain if there are [angles] or [dihedrals] related to those, which you could also delete. You should verify that the final bonds+angles+dihedrals in the topology are what you think they should be. Mark On Fri, Nov 14, 2014 at 8:03 AM, Nixon Raj nixn...@gmail.com wrote: Im dealing a protein with 4799 atoms and 1 ZN ion totally 4800 atoms. I need to form bonds between 4CYS-ZN , where i have equilibrium bond length, force constant and partial charges for the same fixed. Since i have new partial charge for Zn ion , i have created an ZN ion in name ZN1 . My specbond.dat is modified accordingly to add the necessary bonds , CYZ SG 1 ZN1 ZN 1 0.23CYZ ZN1 Running the pdb2gmx yielded me Linking CYZ-210 SG-3368 and ZN1-299 ZN1-4800... Linking CYZ-260 SG-4195 and ZN1-299 ZN1-4800... Linking CYZ-263 SG-4250 and ZN1-299 ZN1-4800... Linking CYZ-270 SG-4358 and ZN1-299 ZN1-4800... Start terminus MET-1: NH3+ End terminus TYR-298: COO- Opening force field file ./charmm36.ff/merged.arn Checking for duplicate atoms Generating any missing hydrogen atoms and/or adding termini. Now there are 299 residues with 4800 atoms Making bonds... Number of bonds was 4859, now 4859 Generating angles, dihedrals and pairs... Before cleaning: 12729 pairs Before cleaning: 12834 dihedrals Keeping all generated dihedrals Making cmap torsions...There are 296 cmap torsion pairs There are 12834 dihedrals, 838 impropers, 8752 angles 12621 pairs, 4859 bonds and 0 virtual sites Total mass 34700.069 a.m.u. Total charge -8.000 e Writing topology But i could find 12 extra bonds created with ZN1(4800) in my topology file. But the dihedrals and angles are in correct numbers. Each residue sharing 4 bonds with ZN1 (4800), i.e) CA-ZN1, HB1-ZN1, HB2-ZN1 and SG-ZN1 , where i need only one bond i.e) SG-ZN1 with each cystein residue. Please help me to cross this roadblock. -- 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. -- 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] How to add a repulsive harmonic potential
Hi, You can use a distance restraint (see manual) implemented with [bonds] type 10. In current released code, the atoms need to be within the same [moleculetype], which would likely mean you need to aggregate the ligands' topology definitions so that you can refer to atoms in different actual molecules that are now within the same [moleculetype] Alternatively, there is draft code for inter-molecular bonded interactions at https://gerrit.gromacs.org/#/c/2566/, but nobody has yet tried that it works. Mark On Fri, Nov 14, 2014 at 10:45 AM, atsutoshi.ok...@takeda.com wrote: Dear all To avoid ligand aggregation under higher concentration, I would like to introduce a weak repulsive potential term between the specific(e.g nitrogen) atoms of ligand molecules in the Protein/Ligand/Water system. This potential set as below. U(R) = K(R-R0)^2, if RR0 (repulsive potential) U(R) = 0, if RR0 Could you tell me how to add the repulsive harmonic potential in MD simulation? Bests, Atsutoshi Okabe -- 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] Flat-bottomed position restraint set
Dear Liuyoung, Remember that the electrostatic screening is much weaker in gas phase systems such as yours. I would use a larger cut-off for the non-bonded interactions to effectively have all vs all interactions. Your system is fairly small so you won't be simulating for that long anyway. Note that gromacs can be told to keep the neighbour list from the first frame, which would speed up things a bit. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Fellow, Fulford JRF Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ On 14 Nov 2014, at 07:15, liuyong_1...@dicp.ac.cnmailto:liuyong_1...@dicp.ac.cn wrote: Hi Justin! I try to apply restraint just to the O atom. There is another question about the set of the coulomb and the vdw interaction for the ion-water cluster Na(H2O)_250. My set is shown as follow: ; vdw vdw-type = Cut-off rvdw= 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = cut-off ;Reaction-Field ;Generalized-Reaction-Field ;cut-off ^M rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm)^M epsilon_rf = 2.0 epsilon_r = 0.5 cutoff-scheme= group The radius of the cluster is about 1.12 nm. Is this set appropriate ? Best regards, Yong Liu liuyong_1...@dicp.ac.cnmailto:liuyong_1...@dicp.ac.cn From: Justin Lemkul Date: 2014-11-14 10:40 To: gmx-users Subject: Re: [gmx-users] Flat-bottomed position restraint set On 11/13/14 7:15 PM, liuyong_1...@dicp.ac.cn wrote: Hi Justin! I use the geometric center of the sphere as the reference coordinates. However, there are still water molecules escaping to the vacuum. Is there other way to aovid this ? This shouldn't happen if things are set up right. Try applying the restraint just to the O atom, not all 3 atoms of the water individually. We do this routinely and it works quite well. -Justin Best regards, Yong Liu liuyong_1...@dicp.ac.cn From: Justin Lemkul Date: 2014-11-12 21:54 To: gmx-users Subject: Re: [gmx-users] Flat-bottomed position restraint set On 11/12/14 8:08 AM, liuyong_1...@dicp.ac.cn wrote: Dear Gromacs users! I use the flat-bottomed position restraints to avoid the molecules to escape from the clusters to the vacuum. The parameters of the restraints on water molecules are shown as follow: #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct g r(nm) k 121 3 30.0 221 3 30.0 321 3 30.0 #endif However, water molecules still escape away from the cluster to the vacuum after about 100 ns MD run at 550K. What should be done with the restraints to avoid the water molecules to escape to the vacuum? Are you using suitable reference coordinates passed to grompp -r? If you're not, then the reference coordinates are whatever is in grompp -c, which means your water molecules can deviate up to 3 nm from that position without penalty. For a sphere, the reference coordinates for the water should be the geometric center of the sphere. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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. -- 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] ramachandran plot
Dear Gromacs users, I generated the ramachandran plot and would like to colour it in xmgrace as it was shown in tutorial: http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html Does anyone know how to do it? Best regards Urszula Uciechowska - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] IMPORTANT
Hi, Please use a descriptive subject. Your email is important to you, but that doesn't help anybody choose whether they might be able to help. :-) On Fri, Nov 14, 2014 at 12:30 PM, Anik Sen anik@kemi.uu.se wrote: Hei, I am using gromacs 4.5 version, Since you are doing new work, you should very likely be using a more recent version of Gromacs, to get faster performance and generally fewer bugs. and i wanted to incorporate a file in the residue. its just a small molecule, h2o2. I had to change the four files in the amber03 forcefield which i was using. atomtypes.atp, ffbonded.itp, ffnonbonded.itp and incorporate a file at the .rtp. Now atomtypes and .rtp file was done with no problem. For ffnonbonded, i had the sigma and epsilon and so it was done. For ffbonded.itp; in the bond types there is are two terms b0 and kb, which i have changed. in the angle types thers is the theta as th0 and another term 'cth'. What is this 'cth' and its unit. For dihedral types what are kd and pn and there units? See the appropriate tables in manual sections in chapter 5 and links therefrom; more recent Gromacs versions have better documentation here, too. Mark I want to know what these terms represent not the value. Thanking you Anik *** STK-14 Uppsala *** https://sites.google.com/site/stkmuu14/ Dr. Anik Sen, Post Doctoral Fellow, Ångströmlaboratoriet- Uppsala Universitet Box 538 SE-751 21 Uppsala Sweden Phone no:- +46-722781705 -- 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.
[gmx-users] What is cth stand for, in the parameters file. It is not written in the latest manual 4.5.6.
What is cth stand for, in the parameters file. It is not written in the latest manual 4.5.6. Is kd the force constant for dihedral angles?? [ bondtypes ] ; ijfunc b0 kb C O 1 0.12300502080. COM1 0.12500418400. .. [ angletypes ] ; i jkfuncth0 cth HOOAC1109.500 397.480 HOOA CH1 1109.500 397.480 .. [ dihedraltypes ] ;i j k l func phase kd pn CA CA CA OH 4 180.00 4.60240 2 with regards Anik Dr. Anik Sen, Post Doctoral Fellow, Ångströmlaboratoriet- Uppsala Universitet Box 538 SE-751 21 Uppsala Sweden Phone no:- +46-722781705 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: 14 November 2014 12:44:02 To: Discussion list for GROMACS users Subject: Re: [gmx-users] IMPORTANT Hi, Please use a descriptive subject. Your email is important to you, but that doesn't help anybody choose whether they might be able to help. :-) On Fri, Nov 14, 2014 at 12:30 PM, Anik Sen anik@kemi.uu.se wrote: Hei, I am using gromacs 4.5 version, Since you are doing new work, you should very likely be using a more recent version of Gromacs, to get faster performance and generally fewer bugs. and i wanted to incorporate a file in the residue. its just a small molecule, h2o2. I had to change the four files in the amber03 forcefield which i was using. atomtypes.atp, ffbonded.itp, ffnonbonded.itp and incorporate a file at the .rtp. Now atomtypes and .rtp file was done with no problem. For ffnonbonded, i had the sigma and epsilon and so it was done. For ffbonded.itp; in the bond types there is are two terms b0 and kb, which i have changed. in the angle types thers is the theta as th0 and another term 'cth'. What is this 'cth' and its unit. For dihedral types what are kd and pn and there units? See the appropriate tables in manual sections in chapter 5 and links therefrom; more recent Gromacs versions have better documentation here, too. Mark I want to know what these terms represent not the value. Thanking you Anik *** STK-14 Uppsala *** https://sites.google.com/site/stkmuu14/ Dr. Anik Sen, Post Doctoral Fellow, Ångströmlaboratoriet- Uppsala Universitet Box 538 SE-751 21 Uppsala Sweden Phone no:- +46-722781705 -- 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. -- 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] energy minimization
Dear md, I think I understand what you want to say. If you want the energy needed to pull away from the binding site, try using Umbrella Sampling method. You will get Potential of Mean Force which you are able to calculate binding constant directly. Best Onur On 11/14/14 08:52 AM, rama david ramadavidgr...@gmail.com wrote: Dear md, On docking the only change in enegy for ligand takes place. The protein is rigid generally. So what was your condition was it regid or flexible for some residues?? so how it can have the energy the energy of single peptide,single protein and the energy of docking complex is compared. The docking complex is not always has so much less energy. which software u used? read the manual of software that may tell about there way to compare the enrgy and algorithm. what is your aim. what u want to say by analysis?? Please mention all these then only someone can suggest you any opinion. With regards, Rama david On Fri, Nov 14, 2014 at 12:06 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/13/14 2:14 AM, md kashif wrote: Dear all Can anyone suggest that how to compare change in energy of my protein before docking and after docking by a ligand. Please suggest any suitable tutorial or paper if possible. You can easily calculate an energy value for the protein (single point energy calculation), but it's not a free energy and it's totally force field-dependent. Proteins are generally (mostly) rigid during docking, so any change in the energy is probably small. If this is related to your previous posts about the energy value after minimization, it's really not a useful quantity because the systems are simply different. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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. Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. Bu e-posta mesaji kisiye özel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which
Re: [gmx-users] What is cth stand for, in the parameters file. It is not written in the latest manual 4.5.6.
On Fri, Nov 14, 2014 at 2:16 PM, Anik Sen anik@kemi.uu.se wrote: What is cth stand for, in the parameters file. It is not written in the latest manual 4.5.6. The angle function *is* documented, in table 5.5, like I said. The notation is inconsistent between that table and the file you are using, but cth is the force constant. Is kd the force constant for dihedral angles?? Yes. See table 5.5 for units. Mark [ bondtypes ] ; ijfunc b0 kb C O 1 0.12300502080. COM1 0.12500418400. .. [ angletypes ] ; i jkfunc th0cth HOOAC1 109.500397.480 HOOA CH1 1109.500 397.480 .. [ dihedraltypes ] ;i j k l func phase kd pn CA CA CA OH 4 180.004.60240 2 with regards Anik Dr. Anik Sen, Post Doctoral Fellow, Ångströmlaboratoriet- Uppsala Universitet Box 538 SE-751 21 Uppsala Sweden Phone no:- +46-722781705 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [ gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Mark Abraham [mark.j.abra...@gmail.com] Sent: 14 November 2014 12:44:02 To: Discussion list for GROMACS users Subject: Re: [gmx-users] IMPORTANT Hi, Please use a descriptive subject. Your email is important to you, but that doesn't help anybody choose whether they might be able to help. :-) On Fri, Nov 14, 2014 at 12:30 PM, Anik Sen anik@kemi.uu.se wrote: Hei, I am using gromacs 4.5 version, Since you are doing new work, you should very likely be using a more recent version of Gromacs, to get faster performance and generally fewer bugs. and i wanted to incorporate a file in the residue. its just a small molecule, h2o2. I had to change the four files in the amber03 forcefield which i was using. atomtypes.atp, ffbonded.itp, ffnonbonded.itp and incorporate a file at the .rtp. Now atomtypes and .rtp file was done with no problem. For ffnonbonded, i had the sigma and epsilon and so it was done. For ffbonded.itp; in the bond types there is are two terms b0 and kb, which i have changed. in the angle types thers is the theta as th0 and another term 'cth'. What is this 'cth' and its unit. For dihedral types what are kd and pn and there units? See the appropriate tables in manual sections in chapter 5 and links therefrom; more recent Gromacs versions have better documentation here, too. Mark I want to know what these terms represent not the value. Thanking you Anik *** STK-14 Uppsala *** https://sites.google.com/site/stkmuu14/ Dr. Anik Sen, Post Doctoral Fellow, Ångströmlaboratoriet- Uppsala Universitet Box 538 SE-751 21 Uppsala Sweden Phone no:- +46-722781705 -- 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. -- 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] Equilibration from Non-shifted to Shifted Potential
I guess I get the idea now. F = -dV(x)/dx. So no time derivative is involved. So shifting the potential would not cause a suddenly impulse on the system. By the way, is Potential-shift the default vdw and coulomb-modifier (so that is used even if i didn't specify a modifier) for gromacs 4.6.7? I didn't see the default value when I searched for vdw-modifier (p.214) of gromacs manual 4.6.7, or when I look at the online manual. coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1 vdwtype = Cut-off vdw-modifier = Potential-shift On Fri, Nov 14, 2014 at 9:31 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Try it and see ;-) mdrun -nsteps 10 -reprod -deffnm shifted mdrun -nsteps 10 -reprod -deffnm not-shifted gmx check -f shifted -f2 not-shifted gmx check -e shifted -e2 not-shifted Alternatively, given that the forces are not computed from the energies (e.g. by central difference or some such), what role does the potential energy play in the integration scheme? :-) Mark On Fri, Nov 14, 2014 at 3:19 PM, Johnny Lu johnny.lu...@gmail.com wrote: Hi. If I change my potential from non-shifted to shift, will the sudden change of energy from non-shifted to shifted potential at step 0 completely mess up the equilibration? Thanks again. -- 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. -- 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.
