[gmx-users] OPLS problem

Christopher Neale chris.neale at alum.utoronto.ca
Fri May 20 19:53:02 CEST 2016

If you want to switch to tip4p but not regenerate your water molecules, then use pdb2gmx to add the dummy MW atom.

It might work with your whole system (I presume  you had to do this anyway, so just use the conf.gro or whatever structure you got from the -o option to pdb2gmx). If that doesnt work for some reason, then do it separately for the water (As below) and then rejoin the new water with your other molecules:

echo "SOL" | gmx trjconv -f start.gro -s start.gro -o water.gro
gmx pdb2gmx -f water.gro -o newwater.gro

From: Steve Seibold <stevesei at ymail.com>
Sent: 20 May 2016 13:37:01
To: Christopher Neale
Subject: Re: [gmx-users] OPLS problem

Thanks Christopher
I was using, as it is recommended, TIP4P. When I switched to TIP3P I no longer get the error. So what do I do if I want to use TIP4P?


On Friday, May 20, 2016 11:06 AM, Christopher Neale <chris.neale at alum.utoronto.ca> wrote:

Did you select tip4p? It has 4 "atoms" per water molecule.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se>> on behalf of Steve Seibold <stevesei at ymail.com<mailto:stevesei at ymail.com>>
Sent: 20 May 2016 11:38
To: gmx-users at gromacs.org<mailto:gmx-users at gromacs.org>
Subject: [gmx-users] OPLS problem

HelloI have gromacs 4.5.4 on one of my machines and have utilizedit many times successfully. However, when I switched force fields to OPLS Istarted getting an error that states "number of coordinates in coordinate filedoes not match topology file". I do not get this error with any other forcefield using the same protein and the same gromacs line commands. I did look on line and in the gromacs errordocumentation and went to my print outs and file.gro file and compared them to thesystem.top files. The number of water and protein residue atoms are the same inthe gro file AND the system.top file exactly. But still I get the above error which reads: "number of coordinatesin coordinate file (99613) does not match topology file (130726)". As I saidthe 99613 is the correct amount of atoms (SOL and Protein) in both gro andsystem.top file. In fact the number 130726 is not found any where in the screenprint outs or the gro files or system.top files... I also made sure that I was not getting a "cpp" error.... Does anyone know what the problem is here???  Steve

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