[gmx-users] Simulating Multiple Solute Particles

[Justin Lemkul]

On 10/26/14 10:49 PM, Nathan K Houtz wrote:
> 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?
>

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

-- 
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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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