Re: [gmx-users] Coul-SR: positive value for interating group
Hi, Indeed. Many force fields in common use are additive, but this is not the same as decomposable! Mark On Wed, May 27, 2015 at 2:52 PM André Farias de Moura mo...@ufscar.br wrote: Raja, just guessing, based on the few informations you posted: if the local dipole moments of these groups are parallel to each other, interaction is expected to be repulsive, even though they have opposite charges. Also mind that overall structure in such complex systems depends on many different interactions, so these two groups are not necessarily close because they have interacted favorably, but because the overall interactions within the whole system eventually led these groups to approach each other, just like groups bearing the same charge pack together in micelles, membranes and films, with large repulsive interactions between the charged heads (stabilization comes from ionic and dipolar screening along with hydrophobic interactions). best Andre On Wed, May 27, 2015 at 3:09 AM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I have just completed simulation of a ligand and enzyme complex and when I visualized the trajectory , I have noted an important close contact say about (7 to 10 A distances) between an active site residue Arg and the carboxylate group of the ligand through out the simulation time of 10ns. I wanted to quantify it using mdrun -rerun option and evaluated energy (COUL-SR) value of the polor atoms of the Arg and carboxylate as energygroup in my mdp file , and surprisingly I found the values are big positive numbers whereas I expected a negative values. Why the contradiction happens , trajectory showed attraction and energy is dispersion ? I just pasted few lines of the energy.xvg @ s0 legend Coul-SR:Arg262_NH-CPG_COOH @ s1 legend Coul-14:Arg262_NH-CPG_COOH 0.005.6473150.00 2.005.3674610.00 4.006.1094620.00 6.000.9768090.00 8.004.3068200.00 10.002.9266590.00 12.002.5676320.00 14.001.9345790.00 16.003.8746910.00 18.003.1305550.00 20.001.8047900.00 expecting you experts opinion on this. Regards, Raja -- 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. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Coul-SR: positive value for interating group
Raja, just guessing, based on the few informations you posted: if the local dipole moments of these groups are parallel to each other, interaction is expected to be repulsive, even though they have opposite charges. Also mind that overall structure in such complex systems depends on many different interactions, so these two groups are not necessarily close because they have interacted favorably, but because the overall interactions within the whole system eventually led these groups to approach each other, just like groups bearing the same charge pack together in micelles, membranes and films, with large repulsive interactions between the charged heads (stabilization comes from ionic and dipolar screening along with hydrophobic interactions). best Andre On Wed, May 27, 2015 at 3:09 AM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I have just completed simulation of a ligand and enzyme complex and when I visualized the trajectory , I have noted an important close contact say about (7 to 10 A distances) between an active site residue Arg and the carboxylate group of the ligand through out the simulation time of 10ns. I wanted to quantify it using mdrun -rerun option and evaluated energy (COUL-SR) value of the polor atoms of the Arg and carboxylate as energygroup in my mdp file , and surprisingly I found the values are big positive numbers whereas I expected a negative values. Why the contradiction happens , trajectory showed attraction and energy is dispersion ? I just pasted few lines of the energy.xvg @ s0 legend Coul-SR:Arg262_NH-CPG_COOH @ s1 legend Coul-14:Arg262_NH-CPG_COOH 0.005.6473150.00 2.005.3674610.00 4.006.1094620.00 6.000.9768090.00 8.004.3068200.00 10.002.9266590.00 12.002.5676320.00 14.001.9345790.00 16.003.8746910.00 18.003.1305550.00 20.001.8047900.00 expecting you experts opinion on this. Regards, Raja -- 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. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Building topologies manually
Dear Gromacs Users, I want to simulate the protein s-glutathionylation. The problem is how to build the topologies for glutathione ([image: $\gamma$]-Glu-Cys-Gly). Could someone give me some suggestion and experiences? Thank in advance Tuong Vy -- 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] gromos53a6_lipid.ff/forcefield.itp not found
From: poncho_8...@hotmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: gromos53a6_lipid.ff/forcefield.itp not found Date: Wed, 27 May 2015 14:50:27 -0300 Hello i'm doing a simulation and when i use grompp grompp -f dppc128.mdp -c dppc128_40ns.pdb -p dppc128.top -o dppc128_1.tpr i have this: Fatal error: Topology include file gromos53a6_lipid.ff/forcefield.itp not found. What should i include in my topolofy files? And i have 2 notes: NOTE 1 [file dppc128.mdp, line 34]: dppc128.mdp did not specify a value for the .mdp option cutoff-scheme. Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Should i inlude Cutoff-scheme verlet in my mdp file? NOTE 2 [file dppc128.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Should i include Berendsen at my Tcouple option on mdp file? -- 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] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
I read more about organic solvents in MD and came to the conclusion that OPLS is indeed the best way to go. Since I couldn’t really find an accessible tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will document my progress here. Maybe this is of help for somebody in the future. In addition, I would like to ask the community to help me in case you see problems with my approach. Once I have a good protocol I will write a tutorial and make it available online. To validate my approach I am trying to create a parameter set for acetone which I found on http://virtualchemistry.org. To generate the OPLS topology I used a tool suggested by many people called mktop in version 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and generated a GROMACS topology file using the following command: mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes In order to get the charges for this organic molecule I downloaded the most recent amber tools and compiled it. I used the AM1-BCC charge model to generate charges for acetone using the following instructions in antechamber: antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2 I opened the resulting mol2 file in Chimera to map the atoms to the atoms in my .top file. The charges calculated by antechamber look reasonable and are comparable to the validated OPLS topology from virtual chemistry: virtual chemistry charges [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_280 1 LIG C 1 0.4712.011 2 opls_135 1 LIG C 2 -0.1812.011 3 opls_135 1 LIG C 3 -0.1812.011 4 opls_281 1 LIG O 4 -0.47 15.9994 5 opls_282 1 LIG H 5 0.06 1.008 6 opls_282 1 LIG H 6 0.06 1.008 7 opls_282 1 LIG H 7 0.06 1.008 8 opls_282 1 LIG H 8 0.06 1.008 9 opls_282 1 LIG H 9 0.06 1.008 10 opls_282 1 LIG H10 0.06 1.008 antechamber AM1-BCC derived [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_280 1 ACN C110.56 12.011 2 opls_281 1 ACN O11 -0.52 15.9994 3 opls_135 1 ACN C22 -0.20 12.011 4 opls_135 1 ACN C33 -0.20 12.011 5 opls_282 1 ACN H120.06 1.008 6 opls_282 1 ACN H220.06 1.008 7 opls_282 1 ACN H320.06 1.008 8 opls_282 1 ACN H430.06 1.008 9 opls_282 1 ACN H530.06 1.008 10 opls_282 1 ACN H630.06 1.008 The atom types were guessed correctly by mktop and also the charge groups make sense I think. So far so good. I realize some differences between the two topologies. First the mktop topology also includes FF constants for the different bonds and angles: [ bonds ] 1 2 1 0.121 476976.0 1 3 1 0.151 265265.6 1 4 1 0.151 265265.6 3 5 1 0.109 284512.0 3 6 1 0.109 284512.0 3 7 1 0.109 284512.0 4 8 1 0.109 284512.0 4 9 1 0.109 284512.0 4 10 1 0.109 284512.0 [ angles ] 1 3 5 1 109.460 292.880 1 3 6 1 109.473 292.880 1 3 7 1 109.484 292.880 1 4 8 1 109.466 292.880 1 4 9 1 109.435 292.880 1 4 10 1 109.477 292.880 2 1 3 1 119.985 669.440 2 1 4 1 119.985 669.440 3 1 4 1 120.029 585.760 5 3 6 1 109.445 276.144 5 3 7 1 109.464 276.144 6 3 7 1 109.502 276.144 8 4 9 1 109.483 276.144 8 4 10 1 109.504 276.144 9 4 10 1 109.462 276.144 compared to the virtual chemistry file: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 2 5 1 2 6 1 2 7 1 3 8 1 3 9 1 310 1 [ angles ] ; aiajak functc0c1c2c3 2 1 3 1 2 1 4 1 3 1 4 1 1 2 5 1 1 2 6 1 1 2 7 1 5 2 6 1 5 2 7 1 6 2 7 1 1 3 8 1 1 3 9 1 1 310 1 8 3 9 1 8 310 1 9 310 1 Should I trust the mktop parameters or delete them? To look if my parameters are correct I did a short MD with a box containing only acetone based on the two topologies. The MD is still running but I wanted to compare the
[gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
Hi there, I am about to setup a water:organic solvent mixture with a protein. I found many organic molecules on http://virtualchemistry.org with definitions for the OPLS FF. However, some are missing so I would need to derive the parameters myself. Before going into more details I was wondering if OPLS is to be preferred if organic solvent is present or can AMBER also be used? It seems that using ACPYPE with AMBER is much more accessible than using any other method to derive the parameters for organic molecules. Thanks for your advice. -- 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] Coul-SR: positive value for interating group
Thank you once again Dr Andre... So to identify the true interaction partner for the ligand's Carboxlate in simulation ...may I have to define the energy group as all amino acids of protein vs the carboxlate group of the ligand or any easy way out ... Since from my trajectory visualization it seemed the Arg 262 is stabilizing the carboxylate of the ligand but the electrostatic interaction analysis disproved it . Regards, Raja On May 27, 2015 8:25 PM, André Farias de Moura mo...@ufscar.br wrote: I agree with Mark: pairwise additive potentials are computationally convenient, but nature does not work like that. based on your email, it is seems that you are looking for an energy/enthalpy term explaining some structural pattern, but in most cases entropy role is also important and in some case might even be the leading contribution. That being said, you should probably consider some sort of PMF instead of looking for specific mechanical interactions. Andre On Wed, May 27, 2015 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Indeed. Many force fields in common use are additive, but this is not the same as decomposable! Mark On Wed, May 27, 2015 at 2:52 PM André Farias de Moura mo...@ufscar.br wrote: Raja, just guessing, based on the few informations you posted: if the local dipole moments of these groups are parallel to each other, interaction is expected to be repulsive, even though they have opposite charges. Also mind that overall structure in such complex systems depends on many different interactions, so these two groups are not necessarily close because they have interacted favorably, but because the overall interactions within the whole system eventually led these groups to approach each other, just like groups bearing the same charge pack together in micelles, membranes and films, with large repulsive interactions between the charged heads (stabilization comes from ionic and dipolar screening along with hydrophobic interactions). best Andre On Wed, May 27, 2015 at 3:09 AM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I have just completed simulation of a ligand and enzyme complex and when I visualized the trajectory , I have noted an important close contact say about (7 to 10 A distances) between an active site residue Arg and the carboxylate group of the ligand through out the simulation time of 10ns. I wanted to quantify it using mdrun -rerun option and evaluated energy (COUL-SR) value of the polor atoms of the Arg and carboxylate as energygroup in my mdp file , and surprisingly I found the values are big positive numbers whereas I expected a negative values. Why the contradiction happens , trajectory showed attraction and energy is dispersion ? I just pasted few lines of the energy.xvg @ s0 legend Coul-SR:Arg262_NH-CPG_COOH @ s1 legend Coul-14:Arg262_NH-CPG_COOH 0.005.6473150.00 2.005.3674610.00 4.006.1094620.00 6.000.9768090.00 8.004.3068200.00 10.002.9266590.00 12.002.5676320.00 14.001.9345790.00 16.003.8746910.00 18.003.1305550.00 20.001.8047900.00 expecting you experts opinion on this. Regards, Raja -- 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. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São
[gmx-users] make_ndx question
Dear all, I am very amateur in GROMACS, so please forgive my silly question. I want to group the following atoms ATOM 2285b C1 LIG X 6 32.880 59.958 110.850 0.00 0.00 ATOM 2285c CL1 LIG X 6 31.972 61.400 110.520 0.00 0.00 ATOM 2285d N1 LIG X 6 32.318 58.744 110.532 0.00 0.00 ATOM 2285e C2 LIG X 6 33.272 57.852 110.816 0.00 0.00 ATOM 2285f N2 LIG X6 34.376 58.450 111.368 0.00 0.00 ATOM 22860 C3 LIG X 6 34.138 59.800 111.370 0.00 0.00 ATOM 22861 C4 LIG X 6 35.550 57.768 111.896 0.00 0.00 ATOM 22862 H1 LIG X 6 35.550 57.880 112.984 0.00 0.00 ATOM 22863 H2 LIG X 6 35.460 56.692 111.730 0.00 0.00 ATOM 22864 C5 LIG X 6 34.992 60.962 111.784 0.00 0.00 ATOM 22865 H3 LIG X 6 35.626 61.290 110.956 0.00 0.00 ATOM 22866 H4 LIG X 6 34.380 61.822 112.070 0.00 0.00 ATOM 22867 O1 LIG X 6 35.840 60.652 112.888 0.00 0.00 ATOM 22868 H5 LIG X 6 36.496 60.016 112.550 0.00 0.00 ATOM 22869 C6 LIG X 6 33.084 56.380 110.604 0.00 0.00 ATOM 2286a H6 LIG X 6 33.950 55.966 110.086 0.00 0.00 ATOM 2286b H7 LIG X 6 33.040 55.868 111.568 0.00 0.00 ATOM 2286c C7 LIG X 6 31.828 56.028 109.792 0.00 0.00 ATOM 2286d H8 LIG X 6 30.938 56.388 110.312 0.00 0.00 ATOM 2286e H9 LIG X 6 31.860 56.538 108.828 0.00 0.00 ATOM 2286f C8 LIG X6 31.688 54.518 109.558 0.00 0.00 ... but the command, a 2285b-2286f or the command, a 2285b 2285c 2285d ... 2286f doesn't recognize atoms' numbers followed by a character Found 0 atoms with names 2285B 2285C Is there any other way that I could select these atoms? I know I could try a dynamic selection (g_select), but unfortunately, my pdb file contains 10 ligands and all of them have the same resname. Thus, there is no feature besides the atom that I could use to destinguish them. Even the coordinates are useless; there are ligands with almost the same x-coordinate but different y. Thanking you in advance! I hope I made clear my problem and didn't confuse you. -- 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] Coul-SR: positive value for interating group
Thank you Dr Andre and Dr Mark for your valuable comments. Regards, Raja On May 27, 2015 6:41 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Indeed. Many force fields in common use are additive, but this is not the same as decomposable! Mark On Wed, May 27, 2015 at 2:52 PM André Farias de Moura mo...@ufscar.br wrote: Raja, just guessing, based on the few informations you posted: if the local dipole moments of these groups are parallel to each other, interaction is expected to be repulsive, even though they have opposite charges. Also mind that overall structure in such complex systems depends on many different interactions, so these two groups are not necessarily close because they have interacted favorably, but because the overall interactions within the whole system eventually led these groups to approach each other, just like groups bearing the same charge pack together in micelles, membranes and films, with large repulsive interactions between the charged heads (stabilization comes from ionic and dipolar screening along with hydrophobic interactions). best Andre On Wed, May 27, 2015 at 3:09 AM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I have just completed simulation of a ligand and enzyme complex and when I visualized the trajectory , I have noted an important close contact say about (7 to 10 A distances) between an active site residue Arg and the carboxylate group of the ligand through out the simulation time of 10ns. I wanted to quantify it using mdrun -rerun option and evaluated energy (COUL-SR) value of the polor atoms of the Arg and carboxylate as energygroup in my mdp file , and surprisingly I found the values are big positive numbers whereas I expected a negative values. Why the contradiction happens , trajectory showed attraction and energy is dispersion ? I just pasted few lines of the energy.xvg @ s0 legend Coul-SR:Arg262_NH-CPG_COOH @ s1 legend Coul-14:Arg262_NH-CPG_COOH 0.005.6473150.00 2.005.3674610.00 4.006.1094620.00 6.000.9768090.00 8.004.3068200.00 10.002.9266590.00 12.002.5676320.00 14.001.9345790.00 16.003.8746910.00 18.003.1305550.00 20.001.8047900.00 expecting you experts opinion on this. Regards, Raja -- 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. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Sigma and Epsilon values for nonbonded interactions with Fe in 2Fe2S cluster
Hi , I am currently doing simulation of Fe dependent enzyme using Amber ff and I too had problem and copied sigma and Epsilon from OPLS ff and so for my simulation goes on fine. Regards, Raja On May 27, 2015 8:42 PM, Jan Riehm jri...@bioinformatik.uni-saarland.de wrote: Dear users, I am using the amber99sb-ildn.ff force field to simulate an adrenodoxin molecule in a water box. In it there is a 2Fe2S cluster which is covalently bound to four surrounding cysteines (two cysteines to each Fe atom). After the first equilibration step (nvt) one of the cysteines clashes or overlaps with the farther apart Fe atom (which is not covalently bound). I've checked for the nonbonded interaction values in the ffnonbonded.itp and the values (sigma and epsilon) for Fe are zero in the [atomtypes]-directive. I am pretty new to this MD simulation stuff and want to know how to derive the values for epsilon and sigma. Or can I look them up anywhere? Any hint to a tutorial would be very helpful! Thank you very much and best regards, Jan -- 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] Coul-SR: positive value for interating group
I agree with Mark: pairwise additive potentials are computationally convenient, but nature does not work like that. based on your email, it is seems that you are looking for an energy/enthalpy term explaining some structural pattern, but in most cases entropy role is also important and in some case might even be the leading contribution. That being said, you should probably consider some sort of PMF instead of looking for specific mechanical interactions. Andre On Wed, May 27, 2015 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Indeed. Many force fields in common use are additive, but this is not the same as decomposable! Mark On Wed, May 27, 2015 at 2:52 PM André Farias de Moura mo...@ufscar.br wrote: Raja, just guessing, based on the few informations you posted: if the local dipole moments of these groups are parallel to each other, interaction is expected to be repulsive, even though they have opposite charges. Also mind that overall structure in such complex systems depends on many different interactions, so these two groups are not necessarily close because they have interacted favorably, but because the overall interactions within the whole system eventually led these groups to approach each other, just like groups bearing the same charge pack together in micelles, membranes and films, with large repulsive interactions between the charged heads (stabilization comes from ionic and dipolar screening along with hydrophobic interactions). best Andre On Wed, May 27, 2015 at 3:09 AM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I have just completed simulation of a ligand and enzyme complex and when I visualized the trajectory , I have noted an important close contact say about (7 to 10 A distances) between an active site residue Arg and the carboxylate group of the ligand through out the simulation time of 10ns. I wanted to quantify it using mdrun -rerun option and evaluated energy (COUL-SR) value of the polor atoms of the Arg and carboxylate as energygroup in my mdp file , and surprisingly I found the values are big positive numbers whereas I expected a negative values. Why the contradiction happens , trajectory showed attraction and energy is dispersion ? I just pasted few lines of the energy.xvg @ s0 legend Coul-SR:Arg262_NH-CPG_COOH @ s1 legend Coul-14:Arg262_NH-CPG_COOH 0.005.6473150.00 2.005.3674610.00 4.006.1094620.00 6.000.9768090.00 8.004.3068200.00 10.002.9266590.00 12.002.5676320.00 14.001.9345790.00 16.003.8746910.00 18.003.1305550.00 20.001.8047900.00 expecting you experts opinion on this. Regards, Raja -- 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. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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] Sigma and Epsilon values for nonbonded interactions with Fe in 2Fe2S cluster
Dear users, I am using the amber99sb-ildn.ff force field to simulate an adrenodoxin molecule in a water box. In it there is a 2Fe2S cluster which is covalently bound to four surrounding cysteines (two cysteines to each Fe atom). After the first equilibration step (nvt) one of the cysteines clashes or overlaps with the farther apart Fe atom (which is not covalently bound). I've checked for the nonbonded interaction values in the ffnonbonded.itp and the values (sigma and epsilon) for Fe are zero in the [atomtypes]-directive. I am pretty new to this MD simulation stuff and want to know how to derive the values for epsilon and sigma. Or can I look them up anywhere? Any hint to a tutorial would be very helpful! Thank you very much and best regards, Jan -- 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] make_ndx question
what about editconf -f orig.pdb -o new.gro followed by figuring out the new residue numbers and running make_ndx on new.gro ? I don't think you'll need the -resnr 1 editconf flag, but if you run into other problems then you might try that. Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Giannis Gl igalda...@gmail.com Sent: 27 May 2015 10:32 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] make_ndx question Dear all, I am very amateur in GROMACS, so please forgive my silly question. I want to group the following atoms ATOM 2285b C1 LIG X 6 32.880 59.958 110.850 0.00 0.00 ATOM 2285c CL1 LIG X 6 31.972 61.400 110.520 0.00 0.00 ATOM 2285d N1 LIG X 6 32.318 58.744 110.532 0.00 0.00 ATOM 2285e C2 LIG X 6 33.272 57.852 110.816 0.00 0.00 ATOM 2285f N2 LIG X6 34.376 58.450 111.368 0.00 0.00 ATOM 22860 C3 LIG X 6 34.138 59.800 111.370 0.00 0.00 ATOM 22861 C4 LIG X 6 35.550 57.768 111.896 0.00 0.00 ATOM 22862 H1 LIG X 6 35.550 57.880 112.984 0.00 0.00 ATOM 22863 H2 LIG X 6 35.460 56.692 111.730 0.00 0.00 ATOM 22864 C5 LIG X 6 34.992 60.962 111.784 0.00 0.00 ATOM 22865 H3 LIG X 6 35.626 61.290 110.956 0.00 0.00 ATOM 22866 H4 LIG X 6 34.380 61.822 112.070 0.00 0.00 ATOM 22867 O1 LIG X 6 35.840 60.652 112.888 0.00 0.00 ATOM 22868 H5 LIG X 6 36.496 60.016 112.550 0.00 0.00 ATOM 22869 C6 LIG X 6 33.084 56.380 110.604 0.00 0.00 ATOM 2286a H6 LIG X 6 33.950 55.966 110.086 0.00 0.00 ATOM 2286b H7 LIG X 6 33.040 55.868 111.568 0.00 0.00 ATOM 2286c C7 LIG X 6 31.828 56.028 109.792 0.00 0.00 ATOM 2286d H8 LIG X 6 30.938 56.388 110.312 0.00 0.00 ATOM 2286e H9 LIG X 6 31.860 56.538 108.828 0.00 0.00 ATOM 2286f C8 LIG X6 31.688 54.518 109.558 0.00 0.00 ... but the command, a 2285b-2286f or the command, a 2285b 2285c 2285d ... 2286f doesn't recognize atoms' numbers followed by a character Found 0 atoms with names 2285B 2285C Is there any other way that I could select these atoms? I know I could try a dynamic selection (g_select), but unfortunately, my pdb file contains 10 ligands and all of them have the same resname. Thus, there is no feature besides the atom that I could use to destinguish them. Even the coordinates are useless; there are ligands with almost the same x-coordinate but different y. Thanking you in advance! I hope I made clear my problem and didn't confuse you. -- 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] gromos53a6_lipid.ff/forcefield.itp not found
Hello i'm doing a simulation and when i use grompp grompp -f dppc128.mdp -c dppc128_40ns.pdb -p dppc128.top -o dppc128_1.tpr i have this: Fatal error: Topology include file gromos53a6_lipid.ff/forcefield.itp not found. What should i include in my topolofy files? And i have 2 notes: NOTE 1 [file dppc128.mdp, line 34]: dppc128.mdp did not specify a value for the .mdp option cutoff-scheme. Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Should i inlude Cutoff-scheme verlet in my mdp file? NOTE 2 [file dppc128.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Should i include Berendsen at my Tcouple option on mdp file? -- 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] g_rdf normalization (-xy option)..
Hi all I'm using g_rdf tool in my system with the option -xy, in order to calculate a cylindrical distribution function. I read the manual and also the help of the tool but I can't find anything about the normalization of this particular result. Could anyone tell me how rdf tool manages the normalization with the option (-xy). I have a long fiber of synthetic polymer, oriented along z direction, and I want to calculate the cylindrical distrib. function from the center of it (backbone). The rdf (cylindrical) shows some peaks which decay to zero at long distances, so I don't understand how the normalization is done. Thank youn in advance -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biológicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 -- 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] Coul-SR: positive value for interating group
Hi, The present analysis says almost nothing about the interaction, neither proof nor disproof. Along with what others have already said, stability is relative to the available alternatives. You can start saying something about stability associated with the arginine if you've e.g. measured the free energy of binding with the arginine vs the free-energy of binding with some similarly sized non-polar residue, for example. That is several orders of magnitude more complex, however... Mark On Wed, 27 May 2015 17:18 Raj D gromacs.fo...@gmail.com wrote: Thank you once again Dr Andre... So to identify the true interaction partner for the ligand's Carboxlate in simulation ...may I have to define the energy group as all amino acids of protein vs the carboxlate group of the ligand or any easy way out ... Since from my trajectory visualization it seemed the Arg 262 is stabilizing the carboxylate of the ligand but the electrostatic interaction analysis disproved it . Regards, Raja On May 27, 2015 8:25 PM, André Farias de Moura mo...@ufscar.br wrote: I agree with Mark: pairwise additive potentials are computationally convenient, but nature does not work like that. based on your email, it is seems that you are looking for an energy/enthalpy term explaining some structural pattern, but in most cases entropy role is also important and in some case might even be the leading contribution. That being said, you should probably consider some sort of PMF instead of looking for specific mechanical interactions. Andre On Wed, May 27, 2015 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Indeed. Many force fields in common use are additive, but this is not the same as decomposable! Mark On Wed, May 27, 2015 at 2:52 PM André Farias de Moura mo...@ufscar.br wrote: Raja, just guessing, based on the few informations you posted: if the local dipole moments of these groups are parallel to each other, interaction is expected to be repulsive, even though they have opposite charges. Also mind that overall structure in such complex systems depends on many different interactions, so these two groups are not necessarily close because they have interacted favorably, but because the overall interactions within the whole system eventually led these groups to approach each other, just like groups bearing the same charge pack together in micelles, membranes and films, with large repulsive interactions between the charged heads (stabilization comes from ionic and dipolar screening along with hydrophobic interactions). best Andre On Wed, May 27, 2015 at 3:09 AM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I have just completed simulation of a ligand and enzyme complex and when I visualized the trajectory , I have noted an important close contact say about (7 to 10 A distances) between an active site residue Arg and the carboxylate group of the ligand through out the simulation time of 10ns. I wanted to quantify it using mdrun -rerun option and evaluated energy (COUL-SR) value of the polor atoms of the Arg and carboxylate as energygroup in my mdp file , and surprisingly I found the values are big positive numbers whereas I expected a negative values. Why the contradiction happens , trajectory showed attraction and energy is dispersion ? I just pasted few lines of the energy.xvg @ s0 legend Coul-SR:Arg262_NH-CPG_COOH @ s1 legend Coul-14:Arg262_NH-CPG_COOH 0.005.6473150.00 2.005.3674610.00 4.006.1094620.00 6.000.9768090.00 8.004.3068200.00 10.002.9266590.00 12.002.5676320.00 14.001.9345790.00 16.003.8746910.00 18.003.1305550.00 20.001.8047900.00 expecting you experts opinion on this. Regards, Raja -- 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. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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
Re: [gmx-users] Variation of distance between 2 CA atoms with time
Please remember: When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... ...and don't reply to the whole digest. On 5/27/15 12:52 AM, Biplab Ghosh wrote: Thank you Justin. I am sorry for not being able to properly pose the problem! I need to know the variation in distance between two residues during the course of the trajectory. I was not sure whether the command was correct or not! The command is correct (for CA-CA distance, which is not necessarily the same as a residue-residue distance). I didn't understand why you thought you hadn't achieved what you wanted. -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.
Re: [gmx-users] Building topologies manually
On 5/27/15 9:41 AM, Vy Phan wrote: Dear Gromacs Users, I want to simulate the protein s-glutathionylation. The problem is how to build the topologies for glutathione ([image: $\gamma$]-Glu-Cys-Gly). Could someone give me some suggestion and experiences? This should be simple to piece together from existing building blocks, but the particular details depend on the force field you're using. That's a key component to the process. -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.
Re: [gmx-users] Sigma and Epsilon values for nonbonded interactions with Fe in 2Fe2S cluster
On 5/27/15 11:22 AM, Raj D wrote: Hi , I am currently doing simulation of Fe dependent enzyme using Amber ff and I too had problem and copied sigma and Epsilon from OPLS ff and so for my simulation goes on fine. Note that those parameters are not official OPLS (and are being removed anyway because of this fact) and certainly shouldn't be copied around between force fields. Just because the simulation doesn't crash doesn't mean it's a valid physical model. The reference for the parameters is given in the .atp file and indicates validation in the context of Fe2+ hydrates and nothing else. The level of theory may be compatible with OPLS, but that remains to be determined. I would not think the same parameters would necessarily be valid for any other Fe-containing prosthetic group. The LJ parameters are probably of less concern than the problems associated with charges in such species. -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.
[gmx-users] iodine non-bonded parameters for charmm36 force field
Hi all, I am trying to build up a model with iodide ion but I don't know where I can obtain those non-bonded parameters for this ion. I am using CHARMM36 force field. Is there any suggestions for that. Thank you. Best Yunlong -- 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] iodine non-bonded parameters for charmm36 force field
On 5/27/15 4:32 PM, Yunlong Liu wrote: Hi all, I am trying to build up a model with iodide ion but I don't know where I can obtain those non-bonded parameters for this ion. I am using CHARMM36 force field. Is there any suggestions for that. Thank you. There aren't any official CHARMM parameters for iodide. -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.
Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2 value on their website) and for the parameter derived as explain in previous mail I got 817.0 which seems too high. Does anybody has an advice how I could improve the derivation of my parameters? Thank you very much, max On May 27, 2015, at 3:25 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: I read more about organic solvents in MD and came to the conclusion that OPLS is indeed the best way to go. Since I couldn’t really find an accessible tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will document my progress here. Maybe this is of help for somebody in the future. In addition, I would like to ask the community to help me in case you see problems with my approach. Once I have a good protocol I will write a tutorial and make it available online. To validate my approach I am trying to create a parameter set for acetone which I found on http://virtualchemistry.org. To generate the OPLS topology I used a tool suggested by many people called mktop in version 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and generated a GROMACS topology file using the following command: mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes In order to get the charges for this organic molecule I downloaded the most recent amber tools and compiled it. I used the AM1-BCC charge model to generate charges for acetone using the following instructions in antechamber: antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2 I opened the resulting mol2 file in Chimera to map the atoms to the atoms in my .top file. The charges calculated by antechamber look reasonable and are comparable to the validated OPLS topology from virtual chemistry: virtual chemistry charges [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_280 1 LIG C 1 0.47 12.011 2 opls_135 1 LIG C 2 -0.18 12.011 3 opls_135 1 LIG C 3 -0.18 12.011 4 opls_281 1 LIG O 4 -0.47 15.9994 5 opls_282 1 LIG H 5 0.06 1.008 6 opls_282 1 LIG H 6 0.06 1.008 7 opls_282 1 LIG H 7 0.06 1.008 8 opls_282 1 LIG H 8 0.06 1.008 9 opls_282 1 LIG H 9 0.06 1.008 10 opls_282 1 LIG H10 0.06 1.008 antechamber AM1-BCC derived [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_280 1 ACN C110.56 12.011 2 opls_281 1 ACN O11 -0.52 15.9994 3 opls_135 1 ACN C22 -0.20 12.011 4 opls_135 1 ACN C33 -0.20 12.011 5 opls_282 1 ACN H120.06 1.008 6 opls_282 1 ACN H220.06 1.008 7 opls_282 1 ACN H320.06 1.008 8 opls_282 1 ACN H430.06 1.008 9 opls_282 1 ACN H530.06 1.008 10 opls_282 1 ACN H630.06 1.008 The atom types were guessed correctly by mktop and also the charge groups make sense I think. So far so good. I realize some differences between the two topologies. First the mktop topology also includes FF constants for the different bonds and angles: [ bonds ] 1 2 1 0.121 476976.0 1 3 1 0.151 265265.6 1 4 1 0.151 265265.6 3 5 1 0.109 284512.0 3 6 1 0.109 284512.0 3 7 1 0.109 284512.0 4 8 1 0.109 284512.0 4 9 1 0.109 284512.0 4 10 1 0.109 284512.0 [ angles ] 1 3 5 1 109.460 292.880 1 3 6 1 109.473 292.880 1 3 7 1 109.484 292.880 1 4 8 1 109.466 292.880 1 4 9 1 109.435 292.880 1 4 10 1 109.477 292.880 2 1 3 1 119.985 669.440 2 1 4 1 119.985 669.440 3 1 4 1 120.029 585.760 5 3 6 1 109.445 276.144 5 3 7 1 109.464 276.144 6 3 7 1 109.502 276.144 8 4 9 1 109.483 276.144 8 4 10 1 109.504 276.144 9 4 10 1 109.462 276.144 compared to the virtual chemistry file: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 3 1 1 4 1 2 5 1 2 6 1 2 7 1 3 8 1 3 9 1 310 1 [ angles ] ; aiajak funct
Re: [gmx-users] gromos53a6_lipid.ff/forcefield.itp not found
On 5/27/15 1:50 PM, Poncho Arvayo Zatarain wrote: Hello i'm doing a simulation and when i use grompp grompp -f dppc128.mdp -c dppc128_40ns.pdb -p dppc128.top -o dppc128_1.tpr i have this: Fatal error: Topology include file gromos53a6_lipid.ff/forcefield.itp not found. What should i include in my topolofy files? So the force field doesn't exist. Either grompp can't find the gromos53a6_lipid.ff directory or it doesn't have forcefield.itp (which would indicate it hasn't been constructed properly). -Justin And i have 2 notes: NOTE 1 [file dppc128.mdp, line 34]: dppc128.mdp did not specify a value for the .mdp option cutoff-scheme. Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Should i inlude Cutoff-scheme verlet in my mdp file? NOTE 2 [file dppc128.mdp]: The Berendsen thermostat does not generate the correct kinetic energy distribution. You might want to consider using the V-rescale thermostat. Should i include Berendsen at my Tcouple option on mdp file? -- == 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.
Re: [gmx-users] iodine non-bonded parameters for charmm36 force field
On 5/27/15 4:32 PM, Yunlong Liu wrote: Hi all, I am trying to build up a model with iodide ion but I don't know where I can obtain those non-bonded parameters for this ion. I am using CHARMM36 force field. Is there any suggestions for that. Thank you. There aren't any official CHARMM parameters for iodide. -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.
Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
On 5/27/15 5:11 PM, Ebert Maximilian wrote: I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2 value on their website) and for the parameter derived as explain in previous mail I got 817.0 which seems too high. Does anybody has an advice how I could improve the derivation of my parameters? Given that the atom types are unchanged and you altered the charges, it suggests that the new charges lead to interactions that are too strong. The balance between LJ and electrostatic terms is key to the balance of the nonbonded interactions in the force field, so either you need to modify LJ terms (not fun) or refine the charges further. Hydration free energy would be another good target data point. -Justin Thank you very much, max On May 27, 2015, at 3:25 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: I read more about organic solvents in MD and came to the conclusion that OPLS is indeed the best way to go. Since I couldn’t really find an accessible tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will document my progress here. Maybe this is of help for somebody in the future. In addition, I would like to ask the community to help me in case you see problems with my approach. Once I have a good protocol I will write a tutorial and make it available online. To validate my approach I am trying to create a parameter set for acetone which I found on http://virtualchemistry.org. To generate the OPLS topology I used a tool suggested by many people called mktop in version 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and generated a GROMACS topology file using the following command: mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes In order to get the charges for this organic molecule I downloaded the most recent amber tools and compiled it. I used the AM1-BCC charge model to generate charges for acetone using the following instructions in antechamber: antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2 I opened the resulting mol2 file in Chimera to map the atoms to the atoms in my .top file. The charges calculated by antechamber look reasonable and are comparable to the validated OPLS topology from virtual chemistry: virtual chemistry charges [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_280 1 LIG C 1 0.4712.011 2 opls_135 1 LIG C 2 -0.1812.011 3 opls_135 1 LIG C 3 -0.1812.011 4 opls_281 1 LIG O 4 -0.47 15.9994 5 opls_282 1 LIG H 5 0.06 1.008 6 opls_282 1 LIG H 6 0.06 1.008 7 opls_282 1 LIG H 7 0.06 1.008 8 opls_282 1 LIG H 8 0.06 1.008 9 opls_282 1 LIG H 9 0.06 1.008 10 opls_282 1 LIG H10 0.06 1.008 antechamber AM1-BCC derived [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB 1 opls_280 1 ACN C11 0.56 12.011 2 opls_281 1 ACN O11 -0.52 15.9994 3 opls_135 1 ACN C22 -0.20 12.011 4 opls_135 1 ACN C33 -0.20 12.011 5 opls_282 1 ACN H120.06 1.008 6 opls_282 1 ACN H220.06 1.008 7 opls_282 1 ACN H320.06 1.008 8 opls_282 1 ACN H43 0.06 1.008 9 opls_282 1 ACN H530.06 1.008 10 opls_282 1 ACN H630.06 1.008 The atom types were guessed correctly by mktop and also the charge groups make sense I think. So far so good. I realize some differences between the two topologies. First the mktop topology also includes FF constants for the different bonds and angles: [ bonds ] 1 2 1 0.121 476976.0 1 3 1 0.151 265265.6 1 4 1 0.151 265265.6 3 5 1 0.109 284512.0 3 6 1 0.109 284512.0 3 7 1 0.109 284512.0 4 8 1 0.109 284512.0 4 9 1 0.109 284512.0 4 10 1 0.109 284512.0 [ angles ] 1 3 5 1 109.460 292.880 1 3 6 1 109.473 292.880 1 3 7 1 109.484 292.880 1 4 8 1 109.466 292.880 1 4 9 1 109.435 292.880 1 4 10 1 109.477 292.880 2 1 3 1 119.985 669.440 2 1 4 1 119.985 669.440 3 1 4 1 120.029 585.760 5 3 6 1 109.445 276.144 5 3 7 1 109.464 276.144 6 3 7 1 109.502 276.144 8 4 9 1 109.483 276.144 8 4 10 1 109.504 276.144 9 4 10 1 109.462 276.144 compared to the virtual chemistry file: [ bonds ] ; aiaj functc0c1c2 c3 1 2 1 1 3 1 1 4 1 2 5 1 2 6 1 2 7 1 3 8 1 3 9 1 310 1
Re: [gmx-users] Is it reasonable to get a bad Ramachandran plot after MD?
Hi Kevin, What happens if you bring the temperature down gradually to experimental (crystallization) conditions? For each residue, what is the proportion of time spent in 'forbidden' regions? Is there a correlation with B-factor? And what would be the effect of the outliers on the experimental observable (the scattering pattern, not the fitted, energy minimized structure)? Cheers, Tsjerk On Wed, May 27, 2015 at 7:43 AM, Kevin C Chan cchan224...@my.cityu.edu.hk wrote: Dear Justin, Thanks for the reply. I was using CHARMM27 force-field. In fact, it was a MDFF simulations in NAMD raising my interest as the resulted structure had 5% outliers and was doubted by experimentalists. I also checked other conventional MD results and the % of outliers vary among structures from 1% to 5% (all using the same CHARMM force-field). I do not know specifically which residues lie in those regions, can anyone suggest a more comprehensive analysis tool for Ramachandran plot? Thanks in advance, Kevin On Fri, May 15, 2015 at 12:41 AM, Justin Lemkul jalem...@vt.edu wrote: On 5/14/15 8:51 AM, Kevin C Chan wrote: Dear Users, As the title states, I am wondering the validity behind the outliers appear in a Ramachandran plot of structure after MD. I only have little data on this, but for a 10,000-atom protein, portion of outlier can increase from 0.7% to 5.0%. Is this explainable? Or it simply means my force-field does not care about the dihedral angles but still accurate enough to predict protein dynamics? Which residues lie in those regions? What force field are you using? Is that force field known to produce only-allowable Ramachandran regions. Note that glycine can do just about anything it likes... -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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] Coul-SR: positive value for interating group
Dear Users, I have just completed simulation of a ligand and enzyme complex and when I visualized the trajectory , I have noted an important close contact say about (7 to 10 A distances) between an active site residue Arg and the carboxylate group of the ligand through out the simulation time of 10ns. I wanted to quantify it using mdrun -rerun option and evaluated energy (COUL-SR) value of the polor atoms of the Arg and carboxylate as energygroup in my mdp file , and surprisingly I found the values are big positive numbers whereas I expected a negative values. Why the contradiction happens , trajectory showed attraction and energy is dispersion ? I just pasted few lines of the energy.xvg @ s0 legend Coul-SR:Arg262_NH-CPG_COOH @ s1 legend Coul-14:Arg262_NH-CPG_COOH 0.005.6473150.00 2.005.3674610.00 4.006.1094620.00 6.000.9768090.00 8.004.3068200.00 10.002.9266590.00 12.002.5676320.00 14.001.9345790.00 16.003.8746910.00 18.003.1305550.00 20.001.8047900.00 expecting you experts opinion on this. Regards, Raja -- 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] Coul-SR: positive value for interating group
Thanks Dr Mark your points are well taken. Regards, Raja On May 28, 2015 1:46 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, The present analysis says almost nothing about the interaction, neither proof nor disproof. Along with what others have already said, stability is relative to the available alternatives. You can start saying something about stability associated with the arginine if you've e.g. measured the free energy of binding with the arginine vs the free-energy of binding with some similarly sized non-polar residue, for example. That is several orders of magnitude more complex, however... Mark On Wed, 27 May 2015 17:18 Raj D gromacs.fo...@gmail.com wrote: Thank you once again Dr Andre... So to identify the true interaction partner for the ligand's Carboxlate in simulation ...may I have to define the energy group as all amino acids of protein vs the carboxlate group of the ligand or any easy way out ... Since from my trajectory visualization it seemed the Arg 262 is stabilizing the carboxylate of the ligand but the electrostatic interaction analysis disproved it . Regards, Raja On May 27, 2015 8:25 PM, André Farias de Moura mo...@ufscar.br wrote: I agree with Mark: pairwise additive potentials are computationally convenient, but nature does not work like that. based on your email, it is seems that you are looking for an energy/enthalpy term explaining some structural pattern, but in most cases entropy role is also important and in some case might even be the leading contribution. That being said, you should probably consider some sort of PMF instead of looking for specific mechanical interactions. Andre On Wed, May 27, 2015 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Indeed. Many force fields in common use are additive, but this is not the same as decomposable! Mark On Wed, May 27, 2015 at 2:52 PM André Farias de Moura mo...@ufscar.br wrote: Raja, just guessing, based on the few informations you posted: if the local dipole moments of these groups are parallel to each other, interaction is expected to be repulsive, even though they have opposite charges. Also mind that overall structure in such complex systems depends on many different interactions, so these two groups are not necessarily close because they have interacted favorably, but because the overall interactions within the whole system eventually led these groups to approach each other, just like groups bearing the same charge pack together in micelles, membranes and films, with large repulsive interactions between the charged heads (stabilization comes from ionic and dipolar screening along with hydrophobic interactions). best Andre On Wed, May 27, 2015 at 3:09 AM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I have just completed simulation of a ligand and enzyme complex and when I visualized the trajectory , I have noted an important close contact say about (7 to 10 A distances) between an active site residue Arg and the carboxylate group of the ligand through out the simulation time of 10ns. I wanted to quantify it using mdrun -rerun option and evaluated energy (COUL-SR) value of the polor atoms of the Arg and carboxylate as energygroup in my mdp file , and surprisingly I found the values are big positive numbers whereas I expected a negative values. Why the contradiction happens , trajectory showed attraction and energy is dispersion ? I just pasted few lines of the energy.xvg @ s0 legend Coul-SR:Arg262_NH-CPG_COOH @ s1 legend Coul-14:Arg262_NH-CPG_COOH 0.005.6473150.00 2.005.3674610.00 4.006.1094620.00 6.000.9768090.00 8.004.3068200.00 10.002.9266590.00 12.002.5676320.00 14.001.9345790.00 16.003.8746910.00 18.003.1305550.00 20.001.8047900.00 expecting you experts opinion on this. Regards, Raja -- 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. -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal
[gmx-users] Making disulfide bonds between protein and glutathion (GSH)
Dear Gromas User, I want to making disulfide bonds between protein and glutathion (GSH). The topology for GSH I got from Produg serve. Could you please show me how I can make the disulfide bons between protein and GSH? Thank you so much Tuong Vy -- 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] Topology for Ligand from Prodrg server and force field 54a7 for protein
Dear Gromacs Users I use the force field 54a7 for protein. Can I simulate the protein-ligand complex with topology of ligand get from PRODRG server. Thanh in advance Tuong Vy -- 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] Building topologies manually
Dear Justin, I am so thankful for your reply. I still do not know how I can build the topology for the [image: $\gamma$] -Glu. I want to use gromos force field 54a7. Could you give some more guideline? Tuong Vy 2015-05-28 5:27 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/27/15 9:41 AM, Vy Phan wrote: Dear Gromacs Users, I want to simulate the protein s-glutathionylation. The problem is how to build the topologies for glutathione ([image: $\gamma$]-Glu-Cys-Gly). Could someone give me some suggestion and experiences? This should be simple to piece together from existing building blocks, but the particular details depend on the force field you're using. That's a key component to the process. -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.
Re: [gmx-users] Water organic solvents mixtures: Which force field to use and best practice to derive parameters
You can try R.E.D. Server. It has more charge models (I don't know whether that will help). Also, IMO, one should target the density and the static dielectric constant when it comes to VDW and partial charges. I saw a recent paper that might be of interest to you http://pubs.acs.org/doi/abs/10.1021/jp3002383 --Mohd Farid Ismail28.05.2015, 05:13, "Ebert Maximilian" m.eb...@umontreal.ca:I just finished a 1 ns NPT calculation of a 2.3x2.3x2.3 nm box filled with acetone (130 molecules). The expected density at 300K is 784.1 kg/m^3. For the virtual chemistry parameters i calculated 798.6 (close to the 800.1±0.2 value on their website) and for the parameter derived as explain in previous mail I got 817.0 which seems too high. Does anybody has an advice how I could improve the derivation of my parameters?Thank you very much,max On May 27, 2015, at 3:25 PM, Ebert Maximilian m.eb...@umontreal.ca wrote: I read more about organic solvents in MD and came to the conclusion that OPLS is indeed the best way to go. Since I couldn’t really find an accessible tutorial how to derive topology files for GROMACS and the FF OPLS/AA I will document my progress here. Maybe this is of help for somebody in the future. In addition, I would like to ask the community to help me in case you see problems with my approach. Once I have a good protocol I will write a tutorial and make it available online. To validate my approach I am trying to create a parameter set for acetone which I found on http://virtualchemistry.org. To generate the OPLS topology I used a tool suggested by many people called mktop in version 2.2.1. I downloaded the ideal geometry of acetone from Ligand Expo and generated a GROMACS topology file using the following command: mktop_2.2.1.pl -i ACN_ideal.pdb -o acn_topology.top -ff opls -conect yes In order to get the charges for this organic molecule I downloaded the most recent amber tools and compiled it. I used the AM1-BCC charge model to generate charges for acetone using the following instructions in antechamber: antechamber -i ACN_ideal.pdb -fi pdb -o acn.mol2 -fo mol2 -c bcc -s 2 I opened the resulting mol2 file in Chimera to map the atoms to the atoms in my .top file. The charges calculated by antechamber look reasonable and are comparable to the validated OPLS topology from virtual chemistry: virtual chemistry charges [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_280 1 LIG C 1 0.47 12.011 2 opls_135 1 LIG C 2 -0.18 12.011 3 opls_135 1 LIG C 3 -0.18 12.011 4 opls_281 1 LIG O 4 -0.47 15.9994 5 opls_282 1 LIG H 5 0.06 1.008 6 opls_282 1 LIG H 6 0.06 1.008 7 opls_282 1 LIG H 7 0.06 1.008 8 opls_282 1 LIG H 8 0.06 1.008 9 opls_282 1 LIG H 9 0.06 1.00810 opls_282 1 LIG H 10 0.06 1.008 antechamber AM1-BCC derived [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB1 opls_280 1 ACN C1 1 0.56 12.0112 opls_281 1 ACN O1 1 -0.52 15.99943 opls_135 1 ACN C2 2 -0.20 12.0114 opls_135 1 ACN C3 3 -0.20 12.0115 opls_282 1 ACN H1 2 0.06 1.0086 opls_282 1 ACN H2 2 0.06 1.0087 opls_282 1 ACN H3 2 0.06 1.0088 opls_282 1 ACN H4 3 0.06 1.0089 opls_282 1 ACN H5 3 0.06 1.008 10 opls_282 1 ACN H6 3 0.06 1.008 The atom types were guessed correctly by mktop and also the charge groups make sense I think. So far so good. I realize some differences between the two topologies. First the mktop topology also includes FF constants for the different bonds and angles: [ bonds ] 1 2 1 0.121 476976.0 1 3 1 0.151 265265.6 1 4 1 0.151 265265.6 3 5 1 0.109 284512.0 3 6 1 0.109 284512.0 3 7 1 0.109 284512.0 4 8 1 0.109 284512.0 4 9 1 0.109 284512.0 4 10 1 0.109 284512.0 [ angles ] 1 3 5 1 109.460 292.880 1 3 6 1 109.473 292.880 1 3 7 1 109.484 292.880 1 4 8 1 109.466 292.880 1 4 9 1 109.435 292.880 1 4 10 1 109.477 292.880 2 1 3 1 119.985 669.440 2 1 4 1 119.985 669.440 3 1 4 1 120.029 585.760 5 3 6 1 109.445 276.144 5 3 7 1 109.464 276.144 6 3 7 1 109.502 276.144 8 4 9 1 109.483 276.144 8 4 10 1 109.504 276.144 9 4 10 1 109.462 276.144 compared to the virtual chemistry file: [ bonds ] ; ai aj funct c0 c1
