[gmx-users] MD simulation with tip5p (with amber99sb)

[Justin Lemkul]

On 10/28/15 1:40 PM, Irem Altan wrote:
> Hi,
>
> I am trying to run an MD simulation with tip5p, using amber99sb. When I look at the folder amber99sb.ff, I see that there exists a tip5p.itp file. However, when I do
>
> pdb2gmx -f 1ytt_refine_001.pdb -ff amber99sb  -o box.gro -p topol.top
>
> I don’t see an option for the water model:
>
> Select the Water Model:
>   1: TIP3P     TIP 3-point, recommended
>   2: TIP4P     TIP 4-point
>   3: TIP4P-Ew  TIP 4-point optimized with Ewald, recommended
>   4: SPC       simple point charge
>   5: SPC/E     extended simple point charge
>   6: None
>
> So I tried the following:
>
> pdb2gmx -f 1ytt_refine_001.pdb -ff amber99sb -water tip5p -o box.gro -p topol.top
>
> which gives the following error:
>
> Residue 'HO5' not found in residue topology database
>
> So then I tried modifying the aminoacids.rtp file in amber99sb.ff, by adding the following:
>
> ; tip5p
> [ HO5 ]
>   [ atoms ]
>      OW  OW             0.00     0
>     HW1  HW             0.241    0
>     HW2  HW             0.241    0
>     MW   MW            -0.241    0
>     MW   MW            -0.241    0
>   [ bonds ]
>     OW   HW1
>     OW   HW1
>
> Which, upon running pdb2gmx -f 1ytt_refine_001.pdb -ff amber99sb -water tip5p -o box.gro -p topol.top   resulted in the following error:
>
> Fatal error:
> There were 384 missing atoms in molecule Water, if you want to use this incomplete topology anyhow, use the option -missing
>
> What am I missing? How can I run an MD simulation with tip5p?
>

You're probably using an old version of GROMACS, because TIP5P was only recently 
added to the list of available water models.  But note that there are issues 
with it that may affect stability. See http://redmine.gromacs.org/issues/134

-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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