[gmx-users] water models

[Justin Lemkul]

On 3/3/16 5:49 PM, Irem Altan wrote:
> The problem is, when I try to do pdb2gmx I get the following error:
>
> Residue 'HO5' not found in residue topology database
>

I already gave my opinion on how to handle this (see the quoted text below).

If you really need to preserve some existing water coordinates, you can run 
pdb2gmx on the water alone to use the HO5 .rtp and .hdb entries to build the 
missing H and lone pairs, then just combine those coordinates with the processed 
protein (which you run through pdb2gmx separately).  Then just use tip5p.itp 
instead of the pdb2gmx-generated water topology that will have bonds and angles 
that you don't want.

-Justin

>
>
> On Mar 3, 2016, at 5:31 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 3/3/16 5:27 PM, Irem Altan wrote:
>
> On Mar 3, 2016, at 5:06 PM, Justin Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 3/3/16 2:21 PM, Irem Altan wrote:
> Hi,
>
> I have two general questions about TIP5P and GROMACS version 5.1.2. (I am
> using AMBER99SB).
>
> - Is it normal that TIP5P does not work out of the box? When I do pdb2gmx
> without modifying force field files, I get an error saying Residue 'HO5' not
> found in residue topology database . This is really confusing, as there
> exists a tip5p.gro, tip5p.itp, the LJ parameters exists within
> ffnonbonded.itp, the atoms are defined in atomtypes.atp, but there is nothing
> within aminoacids.rtp and aminoacids.hdb. Is it meant to be that way?
>
>
> Normally the water topology is simply taken care of by #including the appropriate stock topology.  pdb2gmx will try to create bonds between the atoms, which is not normal for rigid water models.
>
> So am I incorrect in creating relevant entries in aminoacids.rtp and aminoacids.hdb?
>
>
> It certainly won't give you a rigid water model.  Process the protein with pdb2gmx, solvate with the available tip5p.gro and use tip5p.itp to describe the waters.
>
> -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<mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>

-- 
==================================================

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

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