Re: [gmx-users] Query regarding the addition of solvent molecule
Hi, [ molecules ] ; Compound #mols Protein_chain_A 1 CHX3414 Here no water molecules to replace but to neutralize the system I need to replace the solvent ions. As you told I went through the tutorial regarding the genion and addition of ions, but to neutralize solvents apart from water(SOL) I couldnt find enough details. I tried with methanol, then I got Group 13 (MeOH) (instead of SOL) to replace the solvents with the ions in the genion step. But with the solvents I am using like cyclohexane, I am getting only 9 groups and if I try to choose any group its showing error as follows: *Your solvent group size (23449) is not a multiple of 8* I don't know how to resolve this error though I have modified the topology file (.top) with the no. of ions. Kindly need help with this issue. I have attached the screenshot of the error page in the link below. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 Thank you. On Tue, Sep 9, 2014 at 9:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 9:41 AM, Christina Florina wrote: Hi, Thank you for the suggestions. I did the modifications in the .itp file and the grompp step generated the .tpr file successfully. But now, I am facing problem in the genion step, while adding the NA ions the group 13 (usually SOL for water solvent) is not present there. If I select anyother group like system (Grp-1) its showing some fatal error which is not present in gromacs errors and documentation. I have attached the screenshot of the error page (terminal) and the new .itp file (modified) for your reference. Do I need to add the cyclohexane molecule (CHX) in any of the directories to resolve this error? Kindly need help. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 There's no water in your system to replace: [ molecules ] ; Compound#mols Protein_chain_A 1 CHX 3414 I suggest you refer to some tutorial material to understand normal Gromacs workflows and topology organization. There are many linked from the Gromacs website, some of which involve building system with complex/non-water solvents. -Justin On Tue, Sep 9, 2014 at 4:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 7:09 AM, Christina Florina wrote: Hi, Thanks for your suggestions. If the .itp file has error, is there any other way to generate .itp files for the solvents or do i need to write them manually? Because the .itp files I have attached are generated using PRODRG. If I edit the chx.itp file based on the corrections you have told, will it be fine? I am getting the same error for all the 4 solvent files I have generated using PRODRG. I do not get the .itp and .gro files online or tutorials for the organic solvents i am using for my md studies. The only problems I have ever had with PRODRG topologies are charges and charge groups. If you fix those appropriately (charge groups being irrelevant if using the Verlet scheme in Gromacs), that's the only modification you should make. I don't know where all that other stuff came from. I have included the .itp file in both top directory and force field directory. It might be the reason the .gro file could be read in the solvate step. But how to make it in a correct format to proceed with? Solvation doesn't depend on your custom topologies at all. I am new to gromacs using other organic solvents apart from water and default solvents in gromacs package. So, kindly need help how to build an .itp file and .gro file for a solvent and to resolve the issue. Make the changes I indicated in the last message. Read Chapter 5 of the manual for explanations; all of the stuff I pointed out was either (1) syntactically incorrect or (2) not appropriate for the file format. -Justin On Tue, Sep 9, 2014 at 3:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 12:51 AM, Christina Florina wrote: Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regard. Thank you in advance. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/ AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 You have several problems: 1. The #include statement for chx.itp is probably wrong (though I don't know how you're organizing your files), but unless you've put chx.itp in the force field directory, #include gromos43a1.ff/chx.itp is incorrect. 2. The contents of chx.itp are wrong for several reasons. The #ifndef lines are nonsensical and need to be deleted. The #include statement for water needs to be deleted. The [system] and [molecules] levels (which are system-level and thus can only go in a .top
Re: [gmx-users] Query regarding the addition of solvent molecule
Hi, Thanks for your suggestions. If the .itp file has error, is there any other way to generate .itp files for the solvents or do i need to write them manually? Because the .itp files I have attached are generated using PRODRG. If I edit the chx.itp file based on the corrections you have told, will it be fine? I am getting the same error for all the 4 solvent files I have generated using PRODRG. I do not get the .itp and .gro files online or tutorials for the organic solvents i am using for my md studies. I have included the .itp file in both top directory and force field directory. It might be the reason the .gro file could be read in the solvate step. But how to make it in a correct format to proceed with? I am new to gromacs using other organic solvents apart from water and default solvents in gromacs package. So, kindly need help how to build an .itp file and .gro file for a solvent and to resolve the issue. On Tue, Sep 9, 2014 at 3:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 12:51 AM, Christina Florina wrote: Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regard. Thank you in advance. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 You have several problems: 1. The #include statement for chx.itp is probably wrong (though I don't know how you're organizing your files), but unless you've put chx.itp in the force field directory, #include gromos43a1.ff/chx.itp is incorrect. 2. The contents of chx.itp are wrong for several reasons. The #ifndef lines are nonsensical and need to be deleted. The #include statement for water needs to be deleted. The [system] and [molecules] levels (which are system-level and thus can only go in a .top) need to be deleted. -Justin On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 7:10 AM, Christina Florina wrote: Hi, I have included the chx.itp file in the protein.top file already. Checked with the molecule name (CHX) in the .itp file and also in the topology file variable name which matches CHX. But still I am getting the same error. Kindly need help to resolve it. Something doesn't add up. You will need to provide all of your files for download via a file-sharing service to diagnose. A simple #include statement and correct updating of [molecules] is all that is needed. -Justin On Fri, Sep 5, 2014 at 3:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 2:50 AM, Christina Florina wrote: Hi, I have just started my work in MD and using Gromacs 5.0. I need to use cyclohexane as my solvent instead of water. I generated the topology file, .itp and .gro using PRODRG. I have successfully incorporated the .gro file using solvate command and generated the solvent box. But I am facing problem with grompp (ions.mdp) step before the addition of ions. gmx grompp -f ions.mdp -c protein_solv.gro -p protein.top -o ions.tpr I am getting the FATAL ERROR: NO SUCH MOLECULETYPE CHX though I have checked with the molecule name (CHX) in the cyclohexane .itp file. I have tired changing the name of the molecule also. Do I need to add this cyclohexane solvent molecule in the forcefield file or .atp file, .rtp file? I tried adding them but still not able to run this. I might be incorrect while adding it in the .rtp file. So, I kindly need help regarding the addition of new solvent molecule in gromacs since I have other organic solvents also for my md work and having the same problem. You need to #include the CHX .itp file in the system .top, and update [molecules] accordingly. Please note as well that PRODRG topologies are of low quality in my experience and need to be corrected. CHX is simple, a ring of CH2 atom types, all with zero charge. Other results are less trivial to fix. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org
Re: [gmx-users] Query regarding the addition of solvent molecule
Hi, Thank you for the suggestions. I did the modifications in the .itp file and the grompp step generated the .tpr file successfully. But now, I am facing problem in the genion step, while adding the NA ions the group 13 (usually SOL for water solvent) is not present there. If I select anyother group like system (Grp-1) its showing some fatal error which is not present in gromacs errors and documentation. I have attached the screenshot of the error page (terminal) and the new .itp file (modified) for your reference. Do I need to add the cyclohexane molecule (CHX) in any of the directories to resolve this error? Kindly need help. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 On Tue, Sep 9, 2014 at 4:59 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 7:09 AM, Christina Florina wrote: Hi, Thanks for your suggestions. If the .itp file has error, is there any other way to generate .itp files for the solvents or do i need to write them manually? Because the .itp files I have attached are generated using PRODRG. If I edit the chx.itp file based on the corrections you have told, will it be fine? I am getting the same error for all the 4 solvent files I have generated using PRODRG. I do not get the .itp and .gro files online or tutorials for the organic solvents i am using for my md studies. The only problems I have ever had with PRODRG topologies are charges and charge groups. If you fix those appropriately (charge groups being irrelevant if using the Verlet scheme in Gromacs), that's the only modification you should make. I don't know where all that other stuff came from. I have included the .itp file in both top directory and force field directory. It might be the reason the .gro file could be read in the solvate step. But how to make it in a correct format to proceed with? Solvation doesn't depend on your custom topologies at all. I am new to gromacs using other organic solvents apart from water and default solvents in gromacs package. So, kindly need help how to build an .itp file and .gro file for a solvent and to resolve the issue. Make the changes I indicated in the last message. Read Chapter 5 of the manual for explanations; all of the stuff I pointed out was either (1) syntactically incorrect or (2) not appropriate for the file format. -Justin On Tue, Sep 9, 2014 at 3:38 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/14 12:51 AM, Christina Florina wrote: Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regard. Thank you in advance. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/ AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 You have several problems: 1. The #include statement for chx.itp is probably wrong (though I don't know how you're organizing your files), but unless you've put chx.itp in the force field directory, #include gromos43a1.ff/chx.itp is incorrect. 2. The contents of chx.itp are wrong for several reasons. The #ifndef lines are nonsensical and need to be deleted. The #include statement for water needs to be deleted. The [system] and [molecules] levels (which are system-level and thus can only go in a .top) need to be deleted. -Justin On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 7:10 AM, Christina Florina wrote: Hi, I have included the chx.itp file in the protein.top file already. Checked with the molecule name (CHX) in the .itp file and also in the topology file variable name which matches CHX. But still I am getting the same error. Kindly need help to resolve it. Something doesn't add up. You will need to provide all of your files for download via a file-sharing service to diagnose. A simple #include statement and correct updating of [molecules] is all that is needed. -Justin -- 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] Query regarding the addition of solvent molecule
Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regard. Thank you in advance. https://www.dropbox.com/sh/vkvsr3u2hmh2ft9/AABxNv6VxA1gbSs7h2gkaIfxa?dl=0 On Fri, Sep 5, 2014 at 5:25 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 7:10 AM, Christina Florina wrote: Hi, I have included the chx.itp file in the protein.top file already. Checked with the molecule name (CHX) in the .itp file and also in the topology file variable name which matches CHX. But still I am getting the same error. Kindly need help to resolve it. Something doesn't add up. You will need to provide all of your files for download via a file-sharing service to diagnose. A simple #include statement and correct updating of [molecules] is all that is needed. -Justin On Fri, Sep 5, 2014 at 3:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 2:50 AM, Christina Florina wrote: Hi, I have just started my work in MD and using Gromacs 5.0. I need to use cyclohexane as my solvent instead of water. I generated the topology file, .itp and .gro using PRODRG. I have successfully incorporated the .gro file using solvate command and generated the solvent box. But I am facing problem with grompp (ions.mdp) step before the addition of ions. gmx grompp -f ions.mdp -c protein_solv.gro -p protein.top -o ions.tpr I am getting the FATAL ERROR: NO SUCH MOLECULETYPE CHX though I have checked with the molecule name (CHX) in the cyclohexane .itp file. I have tired changing the name of the molecule also. Do I need to add this cyclohexane solvent molecule in the forcefield file or .atp file, .rtp file? I tried adding them but still not able to run this. I might be incorrect while adding it in the .rtp file. So, I kindly need help regarding the addition of new solvent molecule in gromacs since I have other organic solvents also for my md work and having the same problem. You need to #include the CHX .itp file in the system .top, and update [molecules] accordingly. Please note as well that PRODRG topologies are of low quality in my experience and need to be corrected. CHX is simple, a ring of CH2 atom types, all with zero charge. Other results are less trivial to fix. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Query regarding the addition of solvent molecule
Hi, I have included the chx.itp file in the protein.top file already. Checked with the molecule name (CHX) in the .itp file and also in the topology file variable name which matches CHX. But still I am getting the same error. Kindly need help to resolve it. On Fri, Sep 5, 2014 at 3:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/5/14, 2:50 AM, Christina Florina wrote: Hi, I have just started my work in MD and using Gromacs 5.0. I need to use cyclohexane as my solvent instead of water. I generated the topology file, .itp and .gro using PRODRG. I have successfully incorporated the .gro file using solvate command and generated the solvent box. But I am facing problem with grompp (ions.mdp) step before the addition of ions. gmx grompp -f ions.mdp -c protein_solv.gro -p protein.top -o ions.tpr I am getting the FATAL ERROR: NO SUCH MOLECULETYPE CHX though I have checked with the molecule name (CHX) in the cyclohexane .itp file. I have tired changing the name of the molecule also. Do I need to add this cyclohexane solvent molecule in the forcefield file or .atp file, .rtp file? I tried adding them but still not able to run this. I might be incorrect while adding it in the .rtp file. So, I kindly need help regarding the addition of new solvent molecule in gromacs since I have other organic solvents also for my md work and having the same problem. You need to #include the CHX .itp file in the system .top, and update [molecules] accordingly. Please note as well that PRODRG topologies are of low quality in my experience and need to be corrected. CHX is simple, a ring of CH2 atom types, all with zero charge. Other results are less trivial to fix. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
