[gmx-users] TIP5P - water molecules cannot be settled

[Justin Lemkul]

On 3/3/16 5:16 PM, Irem Altan wrote:
> Hi,
>
> Thanks for your reply. I have checked step12b.pdb and step12c.pdb, and I didn’t observe a deformation in the shape of the molecule in question. It doesn’t look like there is any overlap or clash either. I have also tried to comment out the #ifndef FLEXIBLE block and only leave the settles block uncommented. It results in the same error. How can I check if it is the combination of water models and protein force fields that cause the problem?
>

Do people use AMBER + TIP5P often?  Does it run with AMBER + TIP3P?

Also realize that water not being settled doesn't necessarily mean you need to 
troubleshoot the water, it's just that it's the first thing that fails when 
something goes haywire.

-Justin

> Best,
> Irem
>
> On Mar 3, 2016, at 5:01 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 3/3/16 12:51 AM, Irem Altan wrote:
> Hi,
>
> I am using gromacs 5.1.2, and I’m trying to simulate a system that I’ve previously studied with TIP4P and TIP3P, this time using TIP5P. After I solvate the protein and add ions, I try to do energy minimization, but I get the error
>
> step 12: Water molecule starting at atom 5241 can not be settled.
>
> I have added to aminoacids.rtp the following:
>
> ; tip5p
> [ HO5 ]
>   [ atoms ]
>      OW   OW_tip5p      0.00     0
>     HW1   HW            0.24     0
>     HW2   HW            0.24     0
>     LP1   MW           -0.24     0
>     LP2   MW           -0.24     0
>   [ bonds ]
>      OW   HW1
>      OW   HW2
>
> and the following to aminoacids.hdb:
>
> HO5     1
> 4 11 HW OW
>
> My .top file includes the following:
>
> ; Include forcefield parameters
> #include "./amber99sb.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Protein_chain_B.itp"
> #include "topol_Ion_chain_A2.itp"
> #include "topol_Ion_chain_B2.itp"
>
> ; Include water topology
> #include "./amber99sb.ff/tip5p.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 "./amber99sb.ff/ions.itp"
> #include "./tip5pcw.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> Ion_chain_A2        1
> Ion_chain_B2        1
> HO5                96
> HO5                62
> SOL         5681
> NA               6
> CL               10
>
> the included file tip5pcw.itp allows for labeling crystal waters (HO5) and solvation waters (SOL) separately, and its contents are:
>
>
> [ moleculetype ]
> ; molname nrexcl
> HO5             2
>
> [ atoms ]
> ; id  at type     res nr  res name  at name  cg nr  charge    mass
>    1   OW_tip5p    1   HO5       OW       1       0        16.00000
>    2   HW_tip5p    1   HO5       HW1      1       0.241     1.00800
>    3   HW_tip5p    1   HO5       HW2      1       0.241     1.00800
>    4   MW          1   HO5       LP1      1      -0.241     0.00000
>    5   MW          1   HO5       LP2      1      -0.241     0.00000
>
>
> [ bonds ]
> ; i     j funct   length  force.c.
> 1 2 1 0.09572 502416.0 0.09572        502416.0
> 1 3 1 0.09572 502416.0 0.09572        502416.0
>
> [ angles ]
> ; i     j k funct   angle   force.c.
> 2 1 3 1 104.52  628.02  104.52  628.02
>
>
> This means that moleculetype HO5 is flexible, which is probably not stable. Most (if not all) water models are supposed to be rigid during MD.
>
> Beyond that, a whole host of problems could lead to a crash, which may nor may not be related to the water model at all.  Combining TIP5P with protein force fields has caused problems before: http://redmine.gromacs.org/issues/1348
>
> -Justin
>
>
>
> [ virtual_sites3 ]
> ; Vsite from                    funct   a               b               c
> 4      1       2       3       4        -0.344908262    -0.34490826     -6.4437903493
> 5      1       2       3       4        -0.344908262    -0.34490826     6.4437903493
>
>
> [ exclusions ]
> 1 2 3 4 5
> 2 1 3 4 5
> 3 1 2 4 5
> 4 1 2 3 5
> 5 1 2 3 4
>
> What could I be overlooking?
>
> Best,
> Irem
>
>
> --
> ==================================================
>
> 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<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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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

==================================================