Hi, [ molecules ] ; Compound #mols Protein_chain_A 1 CHX 3414
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) 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 >>>>>>> >>>>>>> >>>>>>> > -- > ================================================== > > 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? 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