[gmx-users] Non integer charge for ARG and CYX?

[Eric J. Sorin]

Hi George,

I just quickly checked the partial charges in ARG from the GROMACS v3.3.1 
ffamber03.rtp file and the charges due indeed sum to +1, so I'm not sure why 
you're seeing non-integer total charge in the .rtp file .... it sounds like
you might have a file that was modified by someone and maybe you need to 
update your ffamber files (?).  Please tell me:

Did you get these files from http://chemistry.csulb.edu/ffamber/?
Which version of GROMACS are you using?
Which set of ffamber ports (shown in the top of the .rtp file)?

Thanks!
Eric


----- Original Message ----- 
From: "Georgios Patargias" <    >
To: <gmx-users at gromacs.org>
Sent: Thursday, May 08, 2008 4:09 AM
Subject: [gmx-users] Non integer charge for ARG and CYX?


Hello

Sorry if I address an already covered issue. I happened to notice that
adding up
the ffamber03 partial charges for ARG doesnt yield +1 but ~1.6. Also, for
CYX
the total charge is ~0.87. Is this is a known issue?

In the .itp file, pdb2gmx adds up rounded charge values (as seen in the qtot
column)
and so the total ARG charge comes up to +1 and for CYX 0.

In .tpr, i.e. in the simulation, the full charge values are used, as they
are contained in the
ffamber03.rtp but grompp doesn issu warnings for non-integer total charge
save for rounding
errors.

Thanks in advance.

George



Dr. George Patargias
Polymer IRC Group
University of Leeds
Leeds, LS2 9JT, UK

_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php