Re: [gmx-users] NVT.gro is not genetared
Hi, see the log file for more information and correct the error, it is not recommended to use -maxwarn without knowing the real problem. or share the log file here. -- 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] NVT.gro is not genetared
Dear gmx-users, I'm doing a simulation to a potein- DPPC bilayer system. When tried to run NVT after energy minimization, the following error occurs. --- Program gmx grompp, VERSION 5.1.4 Source code file: /cygdrive/c/Gromacs/src/gromacs/gmxpreprocess/grompp.c, line: 2107 Fatal error: Too many warnings (1), gmx terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- When " maxwarn" is used, the process worked. But after the -" gmx mdrun -deffnm nvt" command the nvt.gro file has not been generated. What can I do to fix this?? -- 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] (no subject)
On 6/27/17 8:11 PM, Shivangi Agarwal wrote: Dear all gromacs users i have to define a new residue, i have added it in *residuetype.dat* file. but still getting error: "residue type not found". Kindly suggest Follow all steps here: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field If you're still having problems, please provide a full description of what you did as well as the full error message reported by pdb2gmx. -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] how we can use Amber ff that are frcmod.hem not present in gromacs
hello everyone i have amber force field for Heme fe---o2 is it possible to convert it to gromacs or we use it as it is in gromacs if we use it then how -- 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] Anybody using Silica InterfaceFF on Gromacs?
This community is mostly focused on other things. If you have solid silica under a non-native (to Gromacs) forcefield and all the bonded parameters have been copied correctly, there may be issues with your partial charges, LJ parameters, and mixing rules. Also make sure your original forcefield uses the same approach to neighbor searching as Gromacs does. Also to my knowledge, very few solid-state potentials use the childish 1-4 pair interaction. Alex On 6/28/2017 11:49 AM, Diez Fernandez, Amanda wrote: Hi, I converted the InterfaceFF silica parameters to use in Gromacs (and to be compatible with the AMBER forcefield) and have gotten some problems, namely I am getting a slightly bigger equilibrium bond length than I should. I was wondering if there were other Gromacs users out there that have used InterfaceFF silica parameters in Gromacs. Many thanks, Amanda -- 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] Anybody using Silica InterfaceFF on Gromacs?
Hi, I converted the InterfaceFF silica parameters to use in Gromacs (and to be compatible with the AMBER forcefield) and have gotten some problems, namely I am getting a slightly bigger equilibrium bond length than I should. I was wondering if there were other Gromacs users out there that have used InterfaceFF silica parameters in Gromacs. Many thanks, Amanda -- 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] Deform a liquid
Hi I am new to gromacs and so a basic doubt. How do we use 'deform' as specified in non equilibrium section of mdp file? Considering I have a box of polymer to be given some shear only in x direction, what should be the arguments? -- Nishi Kashyap Undergraduate Chemical Engineering IIT Delhi -- 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] Using SLLOD to find Viscosity
I have read both things thoroughly. I am new to this and so having a hard time gathering basic concepts. So, correct me if I am wrong: To calculate shear viscosity in a PEG system: 1. Created a stable system and given cos_acceleration =0.05 2. Since I would know A(amplitude of acceleration),rho and k(wave index number), I can find out the viscosity Still, how do I find shear rate from that? Ideally, I should be changing shear rate and finding viscosity. How can I do that ? I might be asking very basic things but please help me here. On Sat, Jun 3, 2017 at 3:25 AM, David van der Spoel wrote: > On 02/06/17 22:12, nishi kashyap wrote: > >> Thanks for replying. >> I have also tried that before. If we give the whole system the same >> acceleration, then it wouldn't experience any shear. That was what I was >> observing also. >> Is there no way/ inbuilt method which use SLLOD , like in LAMMPS ? >> > > Please read my email again carefully, and those references, in particular > the Hess paper. > > > >> On Fri, Jun 2, 2017 at 4:09 PM, David van der Spoel > > >> wrote: >> >> On 02/06/17 22:02, nishi kashyap wrote: >>> >>> Hi I have a system of PEG for which I want to find viscosity. I want to use SLLOD equations to find viscosity for a specific shear rate. I have read allot about different ways , even tried to use 'deform'. But I did not understand what do you mean by "off diagonal elements in a single array". I am not able to understand. And also how do you intend to find shear rate proceeding from that. Could you please give some insight. I would prefer if you just tell me how to use SLLOD equations? I really need it, I have been trying this for so long. Thank You Try using the cos_accel with a few different values. >>> See J. Chem. Phys. 119 pp. 7308-7317 (2003) and J. Chem. Phys. 116, 209 >>> 2002 >>> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >>> Head of Department, Cell & Molecular Biology, Uppsala University. >>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >>> http://www.icm.uu.se >>> -- >>> 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. >>> >>> >> >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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. > -- Nishi Kashyap Undergraduate Chemical Engineering IIT Delhi -- 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] Atom types comparison between CGenFF and Charm36FF
Thanks, Justin. Sure. On Wed, Jun 28, 2017 at 10:21 AM, Justin Lemkul wrote: > > > On 6/28/17 9:10 AM, Mohsen Ramezanpour wrote: > >> Thanks Justin for your comment. >> >> I have a bit of difficulty for the finding the analog parts to these two >> parts. >> >> Is there any database (preferably with shapes) for the molecules available >> in charmmFF? >> >> > The CHARMM topology files have full residue names and chemical structure > drawings. Within the toppar directory (download the tarball from our > site), just grep -r "RESI" * > > If you have additional questions about this or CHARMM parametrization, > contact me off list as this is not really a GROMACS issue. > > > -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. > -- *Rewards work better than punishment ...* -- 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] Atom types comparison between CGenFF and Charm36FF
On 6/28/17 9:10 AM, Mohsen Ramezanpour wrote: Thanks Justin for your comment. I have a bit of difficulty for the finding the analog parts to these two parts. Is there any database (preferably with shapes) for the molecules available in charmmFF? The CHARMM topology files have full residue names and chemical structure drawings. Within the toppar directory (download the tarball from our site), just grep -r "RESI" * If you have additional questions about this or CHARMM parametrization, contact me off list as this is not really a GROMACS issue. -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] gmx wham problem
It looks like you need to sample more states, 13 is not enough. Probably more like 20-30+ would be needed to get a smooth PMF as is discussed in that tutorial. The weird features in your PMF are from insufficiently overlapping histograms, for example the bump near -2.2 nm corresponds to having no histogram there. You also see that you only have one state near -1.2 nm, so that is probably not being sampled enough for WHAM to produce meaningful results. Also I don't understand the meaning of negative distance as a reaction coordinate. If that is the distance between two things, maybe it should be positive. It makes it difficult to understand which values correspond to them being close and far away. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of edesantis [edesan...@roma2.infn.it] Sent: Wednesday, June 28, 2017 10:26 AM To: Gmx users Subject: [gmx-users] gmx wham problem dear all, I am studying the affinity between an antibody and an amyloid peptide; I am interested in the evaluation of the PMF. I have a problem with the PFM shape. I followed the protocol described in the umbrella-sampling tutorial (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html) Here below there is the .mdp part for the pulling ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= Chain_Abeta pull_group2_name= Chains_Antibody pull_coord1_type= umbrella ; harmonic biasing force pull_coord1_geometry= direction pull_coord1_groups = 1 2 pull_coord1_vec = 38.207 68.611 29.8493 pull_coord1_rate= 0.002; 0.01 nm per ps = 10 nm per ns pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 After the pulling simulation, I’ve extracted 13 configuration; for each them, 36 ns of equilibration were performed. These are the mdp directives: ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= Chain_Abeta pull_group2_name= Chains_Antibody pull_coord1_type= umbrella ; harmonic biasing force pull_coord1_geometry= direction pull_coord1_groups = 1 2 pull_coord1_vec = 38.207 68.611 29.8493 pull_coord1_rate= 0.00 pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 Then I ran the wham command: Gmx wham –it list_tpr.dat –if list_pullf.dat -v –b 2 –o –hist And I’ve obtained the following pictures: http://i66.tinypic.com/11t5zdv.png http://i67.tinypic.com/30u8g8x.png Do you have any idea of why the pfm profile has this strange shape? Could it come from any kind of error I’ve made during the simulations? If there are not errors, it seems that the configurations in which the peptide is far from the antibody are more energetically favoured respect to those in contact with the antibody, but I have some doubts about it… Can you help me? Thank you in advance, best regards, Emiliano -- Emiliano De Santis -- 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] gmx wham problem
dear all, I am studying the affinity between an antibody and an amyloid peptide; I am interested in the evaluation of the PMF. I have a problem with the PFM shape. I followed the protocol described in the umbrella-sampling tutorial (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/01_pdb2gmx.html) Here below there is the .mdp part for the pulling ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= Chain_Abeta pull_group2_name= Chains_Antibody pull_coord1_type= umbrella ; harmonic biasing force pull_coord1_geometry= direction pull_coord1_groups = 1 2 pull_coord1_vec = 38.207 68.611 29.8493 pull_coord1_rate= 0.002; 0.01 nm per ps = 10 nm per ns pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 After the pulling simulation, I’ve extracted 13 configuration; for each them, 36 ns of equilibration were performed. These are the mdp directives: ; Pull code pull= yes pull_ngroups= 2 pull_ncoords= 1 pull_group1_name= Chain_Abeta pull_group2_name= Chains_Antibody pull_coord1_type= umbrella ; harmonic biasing force pull_coord1_geometry= direction pull_coord1_groups = 1 2 pull_coord1_vec = 38.207 68.611 29.8493 pull_coord1_rate= 0.00 pull_coord1_k = 1000 ; kJ mol^-1 nm^-2 pull_coord1_start = yes ; define initial COM distance > 0 Then I ran the wham command: Gmx wham –it list_tpr.dat –if list_pullf.dat -v –b 2 –o –hist And I’ve obtained the following pictures: http://i66.tinypic.com/11t5zdv.png http://i67.tinypic.com/30u8g8x.png Do you have any idea of why the pfm profile has this strange shape? Could it come from any kind of error I’ve made during the simulations? If there are not errors, it seems that the configurations in which the peptide is far from the antibody are more energetically favoured respect to those in contact with the antibody, but I have some doubts about it… Can you help me? Thank you in advance, best regards, Emiliano -- Emiliano De Santis -- 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] Atom types comparison between CGenFF and Charm36FF
Thanks Justin for your comment. I have a bit of difficulty for the finding the analog parts to these two parts. Is there any database (preferably with shapes) for the molecules available in charmmFF? Cheers, Mohsen On Tue, Jun 27, 2017 at 7:51 PM, Justin Lemkul wrote: > > > On 6/27/17 3:27 PM, Mohsen Ramezanpour wrote: > >> Dear Gromacs Users, >> >> I am trying to parameterize a molecule in Charmm36FF. >> >> As part of this molecule, there is a "neutral trimethylamine nitrogen" and >> its protonated case. i.e. C-N-C(2) and C-N(H)-C(2), respectively. >> >> To have some idea about the appropriate atom types, I first used the >> GAAMP server. >> >> Here are the assigned atom types by GAAMP (based on CGenFF force field): >> >> >> *For Neutral case:* >> NG301 for N, >> CG3AM0 for two methyl group connected to the N, i.e for bolded Carbons in >> C-N-*C(2).* >> HGA3 for each Hydrogen atom in CG3AM0 methyl groups, >> CG321 for the carbon atom connecting the NC(2) to the rest of molecule. >> i.e. for bolded Carbon in *C*-N-C(2), >> and HGA2 for the Hydrogen atoms connected to CG321. >> ### >> >> *For Protonated case:* >> NG3P1 for N, >> CG334 for two methyl group connected to the N, i.e for bolded Carbons in >> C-N(H)-*C(2).* >> HGA3 for each Hydrogen atom in CG334 methyl groups, >> CG324 for the carbon atom connecting the NC(2) to the rest of molecule. >> i.e. for bolded Carbon in *C*-N(H)-C(2), >> and HGA2 for the Hydrogen atoms connected to CG321. >> >> >> Now, I want to find the best equivalent atom type in Charmm36FF for each >> case. >> >> For the protonated case, I think it is easier as it is something between >> PE >> and PC lipid headgroups. For the neutral case, however, it is difficult to >> find similar atom types in Charmm36. >> >> My approach was to check the LJ and bonded parameters for the assigned >> atom >> types (which are in CGenFF) and find the atom types in Charmm36 with the >> exact same values. Although possible for some cases, but there are many >> problems with this approach: >> >> 1) the exact values are not found in Charmm36FF. >> 2) If it is found, there are a lot of parameters missing in the Charmm36FF >> force field. Not all the bonds, angles, and dihedrals are defined in >> Charmm36FF. >> >> Thanks in advance for any comment or suggestion. >> >> > The "G" in CGenFF is for "general," which means the parameters are not > necessarily the same as the parent CHARMM force field, and are subsequently > a compromise between being highly optimized (e.g. CHARMM36) and being > broadly applicable (general) such that the types can be used across > different molecules. > > If you want to parametrize something for CHARMM, e.g. to be merged into a > larger molecule, you're wasting your time with trying to generate a CGenFF > topology and try to find exact matches in CHARMM36. By definition, you > won't. If your goal is a CHARMM topology, then start from existing CHARMM > atom types, import charges by analogy, and do a full parametrization > procedure (well described in numerous places in the literature). > > -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. > -- *Rewards work better than punishment ...* -- 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] (no subject)
Anyone if have idea, Kindly address On 28 Jun 2017 07:41, "Shivangi Agarwal" wrote: > Dear all gromacs users > > i have to define a new residue, i have added it in *residuetype.dat* file. > but still getting error: "residue type not found". > Kindly suggest > -- > 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] Pram file to gromac converter
Is there any park file converter that convert pram file of amber into gromacs -- 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] Pullin dhiedral angle version 2016
Hello, I’m trying to use the pull code in my RNA system. After a week I was finally able to make it work. But I have some problems This is what I wanted to do: In my system I have a bulge and I would like to se what happen to the rest of the structure if the bulge is completely outside from the double helix or if it is inside it. This is the map file pull-coord1-geometry = dihedral pull-coord1-groups = 1 2 3 4 5 6 pull-group1-pbcatom= 0 pull_group1_name = phospate_6 pull_group2_name = phospate_8 pull_group3_name = phospate_8 pull_group4_name = U7 pull_group5_name = U7 pull_group6_name = bulge pull_coord1_init = -70 pull_coord1_rate = -15 pull_coord1_k = 1000 pull-coord1-start = yes The problem that I have are the following: 1) If the simulation is long and the value for K is very high, the structure breaks and the simulation stops. I think is a problem of boundary conditions. I thought that after the angle is arrived at 180 then it would start automatically to come back… Is this the problem? how can I solve this? 2)when I do the grompp command I noticed also something weird: It says that all the 6 groups have been read, but after the information on the fouler grid it just print 2 groups (the first and the second) giving me these informations: pull group atoms pbc atom distance at start reference at t=0 1 5166 2 523075.082 5.082 Now I now the distance and the reference at t=o, but why it gives me only for the second one? why dose it pick only the middle atoms for the pbc? It should take the COM of the groups. Why it shows only the first 2 groups? Thanks for the help Luca -- 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] Protein-ligand binding Cut-offs
I want to see the closest binding glycine molecules so would "within x distance of any protein atom" be more appropriate? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 28 June 2017 15:13 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-ligand binding Cut-offs Hi, You get to choose... do you want everything within some distance of the protein center of mass, or any protein atom, or something else. But don't be suprrised if there are no ligand atoms super close to the protein center of mass ;-) Mark On Wed, Jun 28, 2017 at 12:47 PM Pandya, Akash wrote: > I assumed it meant to select all ligand molecules closest to the > protein's centre of mass. I'm not entirely sure if that is correct > interpretation. > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 28 June 2017 11:34 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > How are you interpreting "within 4A of my protein?" What has your > protein's center of mass got to do with it? > > Mark > > On Wed, Jun 28, 2017 at 12:16 PM Pandya, Akash > > wrote: > > > Yes it is. So that means I need a cut-off greater than right? > > > > Akash > > > > -Original Message- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > Abraham > > Sent: 28 June 2017 11:08 > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > Is the radius of your protein greater than 0.4 nm? > > > > Mark > > > > On Wed, 28 Jun 2017 12:05 Pandya, Akash > wrote: > > > > > Hi, > > > > > > I want to select all the ligands in my box within 4A of my protein. > > > I looked at gmx help select and I used the command below but > > > nothing appeared. It didn't show my default groups which > > > correspond to the "14" for ligand and "1" for protein. Please advise me > > > on what to do? > > > Am I missing something? > > > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select > > > `group "14" and within 0.4 of com of group "1"' > > > > > > Many thanks, > > > > > > Akash > > > > > > -Original Message- > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > > > Mark Abraham > > > Sent: 21 June 2017 11:56 > > > To: gmx-us...@gromacs.org > > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > > > Hi, > > > > > > You aren't getting output because you aren't actually making a > > > selection - see "gmx help select" and its suggestions for where to > > > look for the rest of the documentation and explained examples. > > > > > > Mark > > > > > > On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash > > > > > > wrote: > > > > > > > I'm not sure if the command I entered (shown below) is correct. > > > > No output was given. I'm unclear as to how this command will > > > > enable me to isolate the glycine molecules within 4A of the > > > > protein > molecule? > > > > > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos > > > > whole_mol_com -seltype dyn_mol_com -pdbatoms all > > > > > > > > Akash > > > > > > > > -Original Message- > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > > > > Mark Abraham > > > > Sent: 16 June 2017 17:22 > > > > To: gmx-us...@gromacs.org > > > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > > > > > Hi, > > > > > > > > Gmx select will produce a selection eg of all molecules with an > > > > atom within a cutoff of any atom in another molecule. > > > > > > > > Mark > > > > > > > > On Fri, 16 Jun 2017 18:15 Pandya, Akash > > > > > > > wrote: > > > > > > > > > Hi all, > > > > > > > > > > I have ran a simulation with a protein and multiple ligand > > > > > molecules inserted randomly inside a box. I want to isolate > > > > > those ligand molecules that are closest to the protein by a > > > > > cut-off of four angstroms or so. Is there a command I could > > > > > use to do this for me or would I have to use a molecular > > > > > visualizer software for > > this? > > > > > > > > > > Thanks, > > > > > > > > > > Akash > > > > > -- > > > > > 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-u > > > > > se
Re: [gmx-users] Number of Contacts
Hi, I used the following command.. gmx mindist -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -od minidist.xvg -on numb_count -d 0.65 By doing this I got this numb_count.xvg graph here https://drive.google.com/open?id=0B99qIEZlZSXfVnQxY3JsUm1rRnc In this number of contacts varying up to 500 which is impossible for my small peptide chain ( two chains in a simulation box and both are seven residue long ). From this I concluded that may be number is so high, because in command line -d 0.65 is not the COM distance. So than I used this gmx select -f ../traj_comp3.xtc -s ../md3.tpr -n index.ndx -select 'group "sd-1" and within 0.65 of com of group "sd-2"' -os size.xvg Where group sd-1 and sd-2 are the side-chain atom index for 1st and 2nd peptide chain. The output by this command is in below link https://drive.google.com/open?id=0B99qIEZlZSXfRDlXN3RaVFROc2s here, output is a size.xvg file which is looking something feasible. I am not sure is that output contains number of inter peptide contacts which I needed or this is something else as the name suggested "size.xvg". Please clear my confusion. Thank you! Sundari On Wed, Jun 28, 2017 at 6:55 AM, Dallas Warren wrote: > First thing you should do when asking for help, is specify exactly > what you have have done (that includes the command line and output), > and then why it is "wrong result". > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > dallas.war...@monash.edu > - > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > On 28 June 2017 at 01:27, Sundari chaudhary wrote: > > Dear all, > > > > I want to calculate the number of inter-peptide and intra-peptide > > side-chain–side-chain contacts and the criteria to form a contact is > that: > > the distance between the centers of mass of two residues is less than a > > specified distance. I tried gmx mindist and gmx distance command lines > but > > i got wrong results. > > > > Please suggest me right command line to do this analysis. > > > > > > Thank you! > > > > Sundari > > -- > > 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] use INTERFACE Force Field
Ok, I did a bit of reading and it may be usable in GROMACS as is. However that doesn't mean that it will be easy to build the topology, as pdb2gmx may not know how to read/work with it. At least the potential energy function is compatible with GROMACS, so that's good news. /J On Wed, Jun 28, 2017 at 4:13 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > If only it was that straightforward. I am not familiar with this INTERFACE > ff, but this is not just about format and layout. There's much more at > stake. However, the team behind it appears to be planning to port it soon: > > "Developments in progress include a graphical user interface to construct > realistic surface models (composition, facet, protonation state) per > mouse-click and to generate automatically simulation input for > inorganic-(bio)organic systems that is compatible with major molecular > dynamics programs (LAMMPS, GROMACS, NAMD, others). Extensions of the force > field and surface models for graphitic structures, bcc/hcp metals, alloys, > organic semiconductors, and other compounds are under way." > > João > > On Wed, Jun 28, 2017 at 3:56 PM, Vytautas Rakeviius < > vytautas1...@yahoo.com> wrote: > >> Hello, >> Possible bot not easy.Look into Gromacs folder share/top/ all force >> fields sit there as text files your will have to make ITERFACE text files >> in same format and layout.What you download as ITERFACE force field are >> also text files with parameters, but layout is for different programs. >> >> >> On Wednesday, June 28, 2017 4:05 PM, Мижээ Батсайхан < >> b.mijidd...@gmail.com> wrote: >> >> >> Dear gmx users, >> >> I would like to use gromacs 5.1v with INTERFACE force field. Please, any >> advice and suggestions, thank you. >> >> Best regards, >> Miji >> -- >> 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] use INTERFACE Force Field
If only it was that straightforward. I am not familiar with this INTERFACE ff, but this is not just about format and layout. There's much more at stake. However, the team behind it appears to be planning to port it soon: "Developments in progress include a graphical user interface to construct realistic surface models (composition, facet, protonation state) per mouse-click and to generate automatically simulation input for inorganic-(bio)organic systems that is compatible with major molecular dynamics programs (LAMMPS, GROMACS, NAMD, others). Extensions of the force field and surface models for graphitic structures, bcc/hcp metals, alloys, organic semiconductors, and other compounds are under way." João On Wed, Jun 28, 2017 at 3:56 PM, Vytautas Rakeviius wrote: > Hello, > Possible bot not easy.Look into Gromacs folder share/top/ all force fields > sit there as text files your will have to make ITERFACE text files in same > format and layout.What you download as ITERFACE force field are also text > files with parameters, but layout is for different programs. > > > On Wednesday, June 28, 2017 4:05 PM, Мижээ Батсайхан < > b.mijidd...@gmail.com> wrote: > > > Dear gmx users, > > I would like to use gromacs 5.1v with INTERFACE force field. Please, any > advice and suggestions, thank you. > > Best regards, > Miji > -- > 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] Protein-ligand binding Cut-offs
Hi, You get to choose... do you want everything within some distance of the protein center of mass, or any protein atom, or something else. But don't be suprrised if there are no ligand atoms super close to the protein center of mass ;-) Mark On Wed, Jun 28, 2017 at 12:47 PM Pandya, Akash wrote: > I assumed it meant to select all ligand molecules closest to the protein's > centre of mass. I'm not entirely sure if that is correct interpretation. > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 28 June 2017 11:34 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > How are you interpreting "within 4A of my protein?" What has your > protein's center of mass got to do with it? > > Mark > > On Wed, Jun 28, 2017 at 12:16 PM Pandya, Akash > wrote: > > > Yes it is. So that means I need a cut-off greater than right? > > > > Akash > > > > -Original Message- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > Abraham > > Sent: 28 June 2017 11:08 > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > Is the radius of your protein greater than 0.4 nm? > > > > Mark > > > > On Wed, 28 Jun 2017 12:05 Pandya, Akash > wrote: > > > > > Hi, > > > > > > I want to select all the ligands in my box within 4A of my protein. > > > I looked at gmx help select and I used the command below but nothing > > > appeared. It didn't show my default groups which correspond to the > > > "14" for ligand and "1" for protein. Please advise me on what to do? > > > Am I missing something? > > > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select > > > `group "14" and within 0.4 of com of group "1"' > > > > > > Many thanks, > > > > > > Akash > > > > > > -Original Message- > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > > Abraham > > > Sent: 21 June 2017 11:56 > > > To: gmx-us...@gromacs.org > > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > > > Hi, > > > > > > You aren't getting output because you aren't actually making a > > > selection - see "gmx help select" and its suggestions for where to > > > look for the rest of the documentation and explained examples. > > > > > > Mark > > > > > > On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash > > > > > > wrote: > > > > > > > I'm not sure if the command I entered (shown below) is correct. No > > > > output was given. I'm unclear as to how this command will enable > > > > me to isolate the glycine molecules within 4A of the protein > molecule? > > > > > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos > > > > whole_mol_com -seltype dyn_mol_com -pdbatoms all > > > > > > > > Akash > > > > > > > > -Original Message- > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > > > > Mark Abraham > > > > Sent: 16 June 2017 17:22 > > > > To: gmx-us...@gromacs.org > > > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > > > > > Hi, > > > > > > > > Gmx select will produce a selection eg of all molecules with an > > > > atom within a cutoff of any atom in another molecule. > > > > > > > > Mark > > > > > > > > On Fri, 16 Jun 2017 18:15 Pandya, Akash > > > > > > > wrote: > > > > > > > > > Hi all, > > > > > > > > > > I have ran a simulation with a protein and multiple ligand > > > > > molecules inserted randomly inside a box. I want to isolate > > > > > those ligand molecules that are closest to the protein by a > > > > > cut-off of four angstroms or so. Is there a command I could use > > > > > to do this for me or would I have to use a molecular visualizer > > > > > software for > > this? > > > > > > > > > > Thanks, > > > > > > > > > > Akash > > > > > -- > > > > > 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-use > > > > > rs 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
Re: [gmx-users] use INTERFACE Force Field
Hello, Possible bot not easy.Look into Gromacs folder share/top/ all force fields sit there as text files your will have to make ITERFACE text files in same format and layout.What you download as ITERFACE force field are also text files with parameters, but layout is for different programs. On Wednesday, June 28, 2017 4:05 PM, Мижээ Батсайхан wrote: Dear gmx users, I would like to use gromacs 5.1v with INTERFACE force field. Please, any advice and suggestions, thank you. Best regards, Miji -- 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] use INTERFACE Force Field
Dear gmx users, I would like to use gromacs 5.1v with INTERFACE force field. Please, any advice and suggestions, thank you. Best regards, Miji -- 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] Protein-ligand binding Cut-offs
I assumed it meant to select all ligand molecules closest to the protein's centre of mass. I'm not entirely sure if that is correct interpretation. Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 28 June 2017 11:34 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-ligand binding Cut-offs How are you interpreting "within 4A of my protein?" What has your protein's center of mass got to do with it? Mark On Wed, Jun 28, 2017 at 12:16 PM Pandya, Akash wrote: > Yes it is. So that means I need a cut-off greater than right? > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 28 June 2017 11:08 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > Is the radius of your protein greater than 0.4 nm? > > Mark > > On Wed, 28 Jun 2017 12:05 Pandya, Akash wrote: > > > Hi, > > > > I want to select all the ligands in my box within 4A of my protein. > > I looked at gmx help select and I used the command below but nothing > > appeared. It didn't show my default groups which correspond to the > > "14" for ligand and "1" for protein. Please advise me on what to do? > > Am I missing something? > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select > > `group "14" and within 0.4 of com of group "1"' > > > > Many thanks, > > > > Akash > > > > -Original Message- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > Abraham > > Sent: 21 June 2017 11:56 > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > Hi, > > > > You aren't getting output because you aren't actually making a > > selection - see "gmx help select" and its suggestions for where to > > look for the rest of the documentation and explained examples. > > > > Mark > > > > On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash > > > > wrote: > > > > > I'm not sure if the command I entered (shown below) is correct. No > > > output was given. I'm unclear as to how this command will enable > > > me to isolate the glycine molecules within 4A of the protein molecule? > > > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos > > > whole_mol_com -seltype dyn_mol_com -pdbatoms all > > > > > > Akash > > > > > > -Original Message- > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of > > > Mark Abraham > > > Sent: 16 June 2017 17:22 > > > To: gmx-us...@gromacs.org > > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > > > Hi, > > > > > > Gmx select will produce a selection eg of all molecules with an > > > atom within a cutoff of any atom in another molecule. > > > > > > Mark > > > > > > On Fri, 16 Jun 2017 18:15 Pandya, Akash > > > > > wrote: > > > > > > > Hi all, > > > > > > > > I have ran a simulation with a protein and multiple ligand > > > > molecules inserted randomly inside a box. I want to isolate > > > > those ligand molecules that are closest to the protein by a > > > > cut-off of four angstroms or so. Is there a command I could use > > > > to do this for me or would I have to use a molecular visualizer > > > > software for > this? > > > > > > > > Thanks, > > > > > > > > Akash > > > > -- > > > > 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-use > > > > rs 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 > >
Re: [gmx-users] Protein-ligand binding Cut-offs
How are you interpreting "within 4A of my protein?" What has your protein's center of mass got to do with it? Mark On Wed, Jun 28, 2017 at 12:16 PM Pandya, Akash wrote: > Yes it is. So that means I need a cut-off greater than right? > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 28 June 2017 11:08 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > Is the radius of your protein greater than 0.4 nm? > > Mark > > On Wed, 28 Jun 2017 12:05 Pandya, Akash wrote: > > > Hi, > > > > I want to select all the ligands in my box within 4A of my protein. I > > looked at gmx help select and I used the command below but nothing > > appeared. It didn't show my default groups which correspond to the > > "14" for ligand and "1" for protein. Please advise me on what to do? > > Am I missing something? > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select `group > > "14" and within 0.4 of com of group "1"' > > > > Many thanks, > > > > Akash > > > > -Original Message- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > Abraham > > Sent: 21 June 2017 11:56 > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > Hi, > > > > You aren't getting output because you aren't actually making a > > selection - see "gmx help select" and its suggestions for where to > > look for the rest of the documentation and explained examples. > > > > Mark > > > > On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash > > > > wrote: > > > > > I'm not sure if the command I entered (shown below) is correct. No > > > output was given. I'm unclear as to how this command will enable me > > > to isolate the glycine molecules within 4A of the protein molecule? > > > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos > > > whole_mol_com -seltype dyn_mol_com -pdbatoms all > > > > > > Akash > > > > > > -Original Message- > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > > Abraham > > > Sent: 16 June 2017 17:22 > > > To: gmx-us...@gromacs.org > > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > > > Hi, > > > > > > Gmx select will produce a selection eg of all molecules with an atom > > > within a cutoff of any atom in another molecule. > > > > > > Mark > > > > > > On Fri, 16 Jun 2017 18:15 Pandya, Akash > > wrote: > > > > > > > Hi all, > > > > > > > > I have ran a simulation with a protein and multiple ligand > > > > molecules inserted randomly inside a box. I want to isolate those > > > > ligand molecules that are closest to the protein by a cut-off of > > > > four angstroms or so. Is there a command I could use to do this > > > > for me or would I have to use a molecular visualizer software for > this? > > > > > > > > Thanks, > > > > > > > > Akash > > > > -- > > > > 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. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting
Re: [gmx-users] Protein-ligand binding Cut-offs
Yes it is. So that means I need a cut-off greater than right? Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 28 June 2017 11:08 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-ligand binding Cut-offs Is the radius of your protein greater than 0.4 nm? Mark On Wed, 28 Jun 2017 12:05 Pandya, Akash wrote: > Hi, > > I want to select all the ligands in my box within 4A of my protein. I > looked at gmx help select and I used the command below but nothing > appeared. It didn't show my default groups which correspond to the > "14" for ligand and "1" for protein. Please advise me on what to do? > Am I missing something? > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select `group > "14" and within 0.4 of com of group "1"' > > Many thanks, > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 21 June 2017 11:56 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > Hi, > > You aren't getting output because you aren't actually making a > selection - see "gmx help select" and its suggestions for where to > look for the rest of the documentation and explained examples. > > Mark > > On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash > > wrote: > > > I'm not sure if the command I entered (shown below) is correct. No > > output was given. I'm unclear as to how this command will enable me > > to isolate the glycine molecules within 4A of the protein molecule? > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos > > whole_mol_com -seltype dyn_mol_com -pdbatoms all > > > > Akash > > > > -Original Message- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > Abraham > > Sent: 16 June 2017 17:22 > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > Hi, > > > > Gmx select will produce a selection eg of all molecules with an atom > > within a cutoff of any atom in another molecule. > > > > Mark > > > > On Fri, 16 Jun 2017 18:15 Pandya, Akash > wrote: > > > > > Hi all, > > > > > > I have ran a simulation with a protein and multiple ligand > > > molecules inserted randomly inside a box. I want to isolate those > > > ligand molecules that are closest to the protein by a cut-off of > > > four angstroms or so. Is there a command I could use to do this > > > for me or would I have to use a molecular visualizer software for this? > > > > > > Thanks, > > > > > > Akash > > > -- > > > 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. > -- > 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
Re: [gmx-users] Protein-ligand binding Cut-offs
Is the radius of your protein greater than 0.4 nm? Mark On Wed, 28 Jun 2017 12:05 Pandya, Akash wrote: > Hi, > > I want to select all the ligands in my box within 4A of my protein. I > looked at gmx help select and I used the command below but nothing > appeared. It didn't show my default groups which correspond to the "14" for > ligand and "1" for protein. Please advise me on what to do? Am I missing > something? > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select `group > "14" and within 0.4 of com of group "1"' > > Many thanks, > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 21 June 2017 11:56 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > Hi, > > You aren't getting output because you aren't actually making a selection - > see "gmx help select" and its suggestions for where to look for the rest of > the documentation and explained examples. > > Mark > > On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash > wrote: > > > I'm not sure if the command I entered (shown below) is correct. No > > output was given. I'm unclear as to how this command will enable me to > > isolate the glycine molecules within 4A of the protein molecule? > > > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos > > whole_mol_com -seltype dyn_mol_com -pdbatoms all > > > > Akash > > > > -Original Message- > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > > Abraham > > Sent: 16 June 2017 17:22 > > To: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > > > Hi, > > > > Gmx select will produce a selection eg of all molecules with an atom > > within a cutoff of any atom in another molecule. > > > > Mark > > > > On Fri, 16 Jun 2017 18:15 Pandya, Akash > wrote: > > > > > Hi all, > > > > > > I have ran a simulation with a protein and multiple ligand molecules > > > inserted randomly inside a box. I want to isolate those ligand > > > molecules that are closest to the protein by a cut-off of four > > > angstroms or so. Is there a command I could use to do this for me or > > > would I have to use a molecular visualizer software for this? > > > > > > Thanks, > > > > > > Akash > > > -- > > > 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. > -- > 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] Protein-ligand binding Cut-offs
Hi, I want to select all the ligands in my box within 4A of my protein. I looked at gmx help select and I used the command below but nothing appeared. It didn't show my default groups which correspond to the "14" for ligand and "1" for protein. Please advise me on what to do? Am I missing something? gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 1 -tu ns -select `group "14" and within 0.4 of com of group "1"' Many thanks, Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: 21 June 2017 11:56 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Protein-ligand binding Cut-offs Hi, You aren't getting output because you aren't actually making a selection - see "gmx help select" and its suggestions for where to look for the rest of the documentation and explained examples. Mark On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash wrote: > I'm not sure if the command I entered (shown below) is correct. No > output was given. I'm unclear as to how this command will enable me to > isolate the glycine molecules within 4A of the protein molecule? > > gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos > whole_mol_com -seltype dyn_mol_com -pdbatoms all > > Akash > > -Original Message- > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark > Abraham > Sent: 16 June 2017 17:22 > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Protein-ligand binding Cut-offs > > Hi, > > Gmx select will produce a selection eg of all molecules with an atom > within a cutoff of any atom in another molecule. > > Mark > > On Fri, 16 Jun 2017 18:15 Pandya, Akash wrote: > > > Hi all, > > > > I have ran a simulation with a protein and multiple ligand molecules > > inserted randomly inside a box. I want to isolate those ligand > > molecules that are closest to the protein by a cut-off of four > > angstroms or so. Is there a command I could use to do this for me or > > would I have to use a molecular visualizer software for this? > > > > Thanks, > > > > Akash > > -- > > 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. -- 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] adding a custom residue with an itp file
Thanks, Justin. I suspected that was the case but I wanted to be 100% sure :D .Jose On Tue, Jun 27, 2017 at 9:48 PM, Justin Lemkul wrote: > > > On 6/27/17 12:32 PM, Jose Borreguero wrote: > >> Dear Gromacs users, >> >> I have created an include topology file (sil.itp) for a silica crystal, >> but >> the instructions in >> http://www.gromacs.org/Documentation/How-tos/Adding_a_ >> Residue_to_a_Force_Field >> leave me with a couple of unclear points. Please help! >> >> 1. This "residue" is not of type 'Protein' or 'DNA', so can I just create >> a >> new type in file residuestypes.dat? Something like "SIL Silica"? Do I >> actually have to declare this molecule within residuestypes.dat? >> >> 2. All the bonding info is already in the sil.itp file I just created, but >> do I still have to include this residue in file aminoacids.rtp? >> >> > You only need aminoacids.rtp and residuetypes.dat if you're running > pdb2gmx. You already have a topology, so there is no purpose to running > pdb2gmx. > > -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.
