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: [EMAIL PROTECTED] εκ μέρους Eric J. Sorin
Αποστολή: Σαβ 5/10/2008 12:48 πμ
Προς: gmx-users@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:
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 listgmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
___
gmx-users mailing listgmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
<>___
gmx-users mailing listgmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
