[gmx-users] TIP3 water problem

[Justin Lemkul]

On 12/20/16 2:41 PM, nikolaev at spbau.ru wrote:
> Hi, all!
>
> I am working with the protein structure with internal waters of TIP3 type,
> and running grompp ends with an error of "No default U-B types", as I
> understand because of some internal inconsistency between atom types (H1,
> H2 and OH2 in my tip3, HW1, HW2, OW in sol). I tried to rename atoms in
> both topol.top and .gro files, add extra .itp file in charmm27.ff, nothing
> worked.
>
> However, this problem has already been mentioned here:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/087725.html
>
> and the solution involved modifying top file (add waters information
> manually). Is it really the only solution of this problem? Because as I
> understand I need to insert manually all the charges, angles, bond lenths
> for all the water molecules. And it seems quite a problem, if I want to
> run more than 1 system.
>

Water molecules should not have [bonds] and [angles] directives because they 
should be treated as rigid via SETTLES.  If your topology has explicit bonds and 
angles, remove them and re-process the coordinates with pdb2gmx to prevent this 
spurious assignment.  Then just #include "tip3p.itp" and list the waters in 
[molecules].

-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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