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

[Georgios Patargias]

Hi Eric 
 
Thanks for your reply. You are right,  the charges in my ffamber03.rtp add up to +1 too. I got the ffamber 2003 ports for gmx331
from the site you mentioned.
 
Actually, it was my mistake. When I transcribed the charges from the ffamber03.rtp to another file I missed the minus sign 
from the N atom...I'm sorry about that. 
 
Thanks again 
George

________________________________

Από: gmx-users-bounces at gromacs.org εκ μέρους Eric J. Sorin
Αποστολή: Σαβ 5/10/2008 12:48 πμ
Προς: gmx-users at gromacs.org
Θέμα: Re: [gmx-users] Non integer charge for ARG and CYX?



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

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