[gmx-users] moleculaes breaking off after EM - help
Justin Lemkul
jalemkul at vt.edu
Wed Oct 5 14:30:56 CEST 2016
On 10/5/16 12:11 AM, Thejus Kartha wrote:
> Thanks, Dr. Lemkul, for your assistance. Here's my topology file, for 512 atoms. Please tell me where I'm going wrong in this. Frankly, I can't find issues with this, even after comparing it with any other topology file created by GROMACS itself. Please go through it and let me know.--------------------------------Topology file------------------------------------------------------------
> ;
> ;
> ; This file was generated by PRODRG version AA100323.0717
> ; PRODRG written/copyrighted by Daan van Aalten
> ; and Alexander Schuettelkopf
> ;
> ; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> ;
> ; When using this software in a publication, cite:
> ; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> ; PRODRG - a tool for high-throughput crystallography
> ; of protein-ligand complexes.
> ; Acta Crystallogr. D60, 1355--1363.
> ;
> ;
>
> ; Include forcefield parameters
> #include "gromos43a1.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> LIG 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 CH1 1 LIG CAA 1 0.070 14.0270
> 2 OA 1 LIG OAB 1 -0.140 15.9994
> 3 CH1 1 LIG CAC 1 0.070 14.0270
> 4 CH1 1 LIG CAD 1 0.070 14.0270
> 5 OA 1 LIG OAE 1 -0.140 15.9994
> 6 CH1 1 LIG CAF 1 0.070 14.0270
>
For dioxane, the atom types for the carbons should all be CH2. I can't vouch
for the charges, but you should validate the topology based on available target
data, e.g. free energy of hydration before proceeding.
Otherwise, what I said before remains valid - do the in vacuo test. If that
works, then whatever you did to the coordinates for the condensed phase system
was bad.
-Justin
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 1 2 2 0.144 6100000.0 0.144 6100000.0 ; CAA OAB
> 1 6 2 0.152 5430000.0 0.152 5430000.0 ; CAA CAF
> 3 2 2 0.144 6100000.0 0.144 6100000.0 ; CAC OAB
> 3 4 2 0.152 5430000.0 0.152 5430000.0 ; CAC CAD
> 4 5 2 0.144 6100000.0 0.144 6100000.0 ; CAD OAE
> 6 5 2 0.144 6100000.0 0.144 6100000.0 ; CAF OAE
>
> [ pairs ]
> ; ai aj fu c0, c1, ...
> 1 4 1 ; CAA CAD
> 2 5 1 ; OAB OAE
> 3 6 1 ; CAC CAF
>
> [ angles ]
> ; ai aj ak fu c0, c1, ...
> 2 1 6 2 109.5 520.0 109.5 520.0 ; OAB CAA CAF
> 1 2 3 2 109.5 380.0 109.5 380.0 ; CAA OAB CAC
> 2 3 4 2 109.5 520.0 109.5 520.0 ; OAB CAC CAD
> 3 4 5 2 109.5 520.0 109.5 520.0 ; CAC CAD OAE
> 4 5 6 2 109.5 380.0 109.5 380.0 ; CAD OAE CAF
> 1 6 5 2 109.5 520.0 109.5 520.0 ; CAA CAF OAE
>
> [ dihedrals ]
> ; ai aj ak al fu c0, c1, m, ...
> 6 1 2 3 1 0.0 3.8 3 0.0 3.8 3 ; dih CAF CAA OAB CAC
> 5 6 1 2 1 0.0 5.9 3 0.0 5.9 3 ; dih OAE CAF CAA OAB
> 4 3 2 1 1 0.0 3.8 3 0.0 3.8 3 ; dih CAD CAC OAB CAA
> 5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih OAE CAD CAC OAB
> 3 4 5 6 1 0.0 3.8 3 0.0 3.8 3 ; dih CAC CAD OAE CAF
> 1 6 5 4 1 0.0 3.8 3 0.0 3.8 3 ; dih CAA CAF OAE CAD
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "gromos43a1.ff/tip4p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
>
> [ system ]
> ; Name
> Dioxane_10%
>
> [ molecules ]
> ; Compound #mols
> LIG 512-----------------------------------------------------------------------------------------------------------------
>
> If you can't find anything wrong with it, I guess I should redo my genconf command. Isn't it?
> Thanks & regards,Thejus Kartha
>
>
> On Monday, 3 October 2016 5:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 10/2/16 10:09 PM, Thejus Kartha wrote:
>> Greetings!
>> I was performing an EM run with an array of dioxane molecules, for which I had produced co-ordinates from PRODRG. I got the co-ordinates, and made an array of it, using the gmx genconf module, and corrected my topology file. Then, I thought I should minimize the energy of this array before solvating it, or anything. So, as I was running the grompp module using mdp files from Dr. Lemkul's tutorials, it gave me the following error:
>> Steepest Descents converged to machine precision in 641 steps,
>> but did not reach the requested Fmax < 1000.
>> Potential Energy = 2.6059185e+09
>> Maximum force = 8.6477500e+04 on atom 557
>> Norm of force = 7.7685435e+03
>>
>> I am presuming there's something seriously wrong with my input files, as I've been told many times before. That said, how do I tweak around with my mdp file in this case? I mean, there's this Fmax value that I have to deal with. How do I know if I am using the right threshold for Fmax? Do I base this value on information from literature? And of course, when I open the .gro file after the EM, I find my molecules to be smashed to smithereens. There are points and broken triangles flying around in all directions (dioxane is a hexagon, and it has broken to half.) Why does this happen? Please help me.
>
> This suggests your topology is wrong. Test with one molecule in vacuo. If it
> does the same thing, fix the topology. If the in vacuo test goes well, then
> your coordinates in the assembled box are unreasonable.
>
> -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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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