Sorry everybody, I accidentally unsubscribed from the mailing list and missed my last response. Dr. Lemkul posted a message but I can't reply directly to it, so here's what he said:
>Your topology is constructed incorrectly, but without seeing it in its >entirety, it is impossible to say. Please post the file for download somewhere >and provide a link, otherwise copy and paste its entire contents into a reply >if the message will be small enough. > > >-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 Thank you Justin! I think it's easier to just paste it here. This is my topol.top file: >[ defaults ] >; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 0.5 > >[ atomtypes ] >;name at.num mass charge ptype sigma epsilon > CH3 15 15.03500 0.000 A 0.39100 0.66944 > ;united atom Methyl [C-CH3] > C 12 12.01100 0.000 A 0.35000 0.27614 ;C > [R3CCOO-] (first carbon) > CM 12 12.01100 0.000 A 0.37500 0.43932 > ;carboxyl C [R-(C=O)-OH] > O 8 15.99940 0.000 A 0.30800 0.71128 > ;carboxyl O [C-O-H] > OM 8 15.99940 0.000 A 0.29600 0.87864 > ;carbonyl O [C=O] > H 1 1.00794 0.000 A 0.00000 0.00000 > ;carboxyl H [C-O-H] > OW 8 15.99940 0.000 A 0.31660 0.65000 > HW 1 1.00794 0.000 A 0.00000 0.00000 > >[ moleculetype ] >; Name nrexcl > TETR 3 > >[ atoms ] >; nr type resnr residu atom cgnr charge mass > 1 CH3 1 TETR C1 1 0 15.03500 > 2 C 1 TETR C2 1 0 12.01100 > 3 C 1 TETR C3 1 0 12.01100 > 4 CM 1 TETR C4 1 0.38 12.01100 > 5 OM 1 TETR O1 1 -0.38 15.99940 > 6 O 1 TETR O2 1 -0.40 15.99940 > 7 H 1 TETR H4 1 0.40 1.00794 > >[constraints] >; i j funct distance > 1 2 1 0.14550 > 2 3 1 0.11780 > 3 4 1 0.14420 > 4 5 1 0.12040 > 4 6 1 0.13100 > 6 7 1 0.89000 > >; Include SPC water topology >#include "oplsaa.ff/tip3p.itp" > >[ system ] >Tetrolic Acid in water > >[ molecules ] >Tetrolic Acid 500 >SOL 5481 I made the file myself, so I hope I didn't make any syntax errors. I discovered with the .gro file that the spacing is very important since gromacs doesn't use delimiters but allows only a fixed number of characters for each entry. Is the .top file the same way? I just used a template from some example file and tried to make the numbers fit appropriately under the headings. If it's not correct, why didn't gromacs complain when I solvated it? Doesn't it read in the topology file then as well? I'm subscribed again so I won't miss a reply. Thanks again for the guidance! N. H. ----- Original Message ----- From: "Nathan K Houtz" <nho...@purdue.edu> To: gmx-us...@gromacs.org Sent: Sunday, October 26, 2014 10:49:35 PM Subject: Re: [gmx-users] Simulating Multiple Solute Particles Thanks for your help. And actually my version of gromacs does not have genbox anymore. (http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 at the bottom: GENBOX - This tool has been split to gmx solvate and gmx insert-molecules.) But it's no big deal, insert-molecules seemed to work just fine! Here are the commands I used: >>gmx insert-molecules -f tetrolic_acid.gro -ci tetrolic_acid.gro -nmol 499 -o >>tetrolic500.gro >>gmx solvate -cp tetrolic500.gro -cs spc216.gro -o tetrolic_solv.gro -p >>topol.top where tetrolic_acid.gro and topol.top are files I created myself to define the molecule. I checked the output in vmd and it looks like exactly what I want. But now I'm stuck on another step and I get a confusing error. I tried to minimize the energy via: >>gmx grompp -f minim.mdp -c tetrolic_solv.gro -p topol.top -o em.tpr I stole the minim.mdp file from a tutorial (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp). I don't know how to properly create an mdp file from scratch, but judging from the comments, it seems reasonable and I don't see anything that must be specific to the case in the tutorial. Anyway, I don't think it caused my error. The output for that command is: Fatal error: Atomtype opls_111 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The link is not helpful, however. Googling exactly the error turns up very few results. The problem seems to be either with my topology file or with the itp file for water, which is referenced in my topology file like this: #include "oplsaa.ff/tip3p.itp" right after the constraints section. I also tried <#include "oplsaa.ff/spc.itp"> but it came up with a nearly identical error: Fatal error: Atomtype opls_116 not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors The closest thing to help I found by searching was this blog post: http://www.somewhereville.com/?p=114 However, his initial spc.itp file looks much different than mine. I think he must just have an older version of gromacs or something. Does anyone else know how I could do the energy minimization? Thanks again for all your help! N.H. ----- Original Message ----- From: "Mark Abraham" <mark.j.abra...@gmail.com> To: "Discussion list for GROMACS users" <gmx-us...@gromacs.org> Sent: Saturday, October 25, 2014 6:10:21 AM Subject: Re: [gmx-users] Simulating Multiple Solute Particles On Sat, Oct 25, 2014 at 7:23 AM, Nathan K Houtz <nho...@purdue.edu> wrote: > Hello, I apologize for any ignorance but I'm quite new to gromacs and am > confused about a few things. > > I want to run some simulations of a small molecule, tetrolic acid > (CH3-C≡C-COOH) dissolved in a box of water. I'm doing this to see if a > united atom approximation on the methyl group is sufficiently good for > saving a bit of computation time. I have created a .gro file and a .top > file and attempted to put it into gromacs but I don't know how to model > more than one molecule of TTA. All of the tutorials I've looked up involve > solvating enormous proteins and they only do one at a time. I'd like to > simulate hundreds of TTA molecules with an appropriate amount of water > molecules. I attempted to do this by specifying the numbers of TTA and H2O > in my topology file, but when I tried to solvate it, gromacs removed the > line specifying how many waters and replaced it with its own number (216) > and made the box way too small to fit any more TTA. I feel like this may be > trivial, but I'm stuck. I really appreciate anyone's help. > You can adapt http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents to do this. > After I figure this out, I'm going to try do dissolve tetrolic acid in > chloroform, then ethanol as well. I suspect gromacs doesn't have a built in > .gro or .top files for either of those (certainly not chloroform). Would > the solvate command work just as well if I created my own? > Yes, but perhaps gmx solvate -p won't quite do what you want. Do equilbrate that box decently; garbage in -> garbage out. Mark > Thanks in advance! > N.H. > -- > 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? 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