Thank you very much, Alan.
In this case, I am not using acpypi, since I am using a topology for dopc
already published, and it is already converted into Gromacs. So, it´s
manually, as you suppose. I will follow your suggestion and change c and o by
c_ and o_.
Best wishes,
Rebeca.
From: alanwil...@gmail.com
Date: Thu, 4 Jun 2009 22:19:30 +0100
To: gmx-users@gromacs.org
Subject: [gmx-users] Re: goverrriding problem
Yep, contrary to AMBER, GMX is not case sensitive, so C and c are the same and
since you declare them twice you get this overriding warning.
However, I did acpypi aware of this (it should add '_' to e.g. c, making 'c_').
Unless you're doing something manually (as it seems). Otherwise it would a
pleasure to see this issue closely (can you send me your input prmtop and
inpcrd?).
Otherwise do it yourself by making c_ and o_ and the overriding warn will be
off.
Cheers,
Alan
Message: 7
Date: Thu, 4 Jun 2009 20:55:52 +0000
From: Rebeca Garc?a Fandi?o <rega...@hotmail.com>
Subject: [gmx-users] overrriding problem
To: <gmx-users@gromacs.org>
Message-ID: <bay142-w269f0995d7f3b4890e330db7...@phx.gbl>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I am doing a simulation combining amber and Gaff force field (for dopc lipids),
this is the first part of my topology file:
; UNK_GMX.top created by acpypi on Thu Jun 4 22:06:03 2009
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91
0.0860
CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91
0.1094
C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91
0.0860
HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00
0.0000
O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66
0.2100
OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72
0.2104
c3 c3 12.0100 -0.12654 A 3.399676e-01
4.577296e-01 ; 1.91 0.1094
hc hc 1.0080 0.02245 A 2.649538e-01
6.568880e-02 ; 1.49 0.0157
c2 c2 12.0100 -0.15458 A 3.399676e-01
3.598240e-01 ; 1.91 0.0860
ha ha 1.0080 0.11146 A 2.599647e-01
6.276000e-02 ; 1.46 0.0150
c c 12.0100 0.44800 A 3.399676e-01
3.598240e-01 ; 1.91 0.0860
o o 16.0000 -0.47180 A 2.959927e-01
8.786400e-01 ; 1.66 0.2100
os os 16.0000 -0.15429 A 3.000018e-01
7.112800e-01 ; 1.68 0.1700
h1 h1 1.0080 0.16551 A 2.471358e-01
6.568880e-02 ; 1.39 0.0157
p5 p5 30.9700 1.14364 A 3.741781e-01
8.368000e-01 ; 2.10 0.2000
n4 n4 14.0100 0.01626 A 3.250004e-01
7.112800e-01 ; 1.82 0.1700
hx hx 1.0080 0.08244 A 1.959981e-01
6.568880e-02 ; 1.10 0.0157
OW OW 0.00000 0.00000 A 3.16572e-01 6.49775e-01 ;
1.78 0.1553
HW HW 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ;
0.00 0.0000
Na Na 0.00000 0.00000 A 2.15954e-01 1.47545e+00 ; 1.21
0.3526
Cl Cl 0.00000 0.00000 A 4.83045e-01 5.34924e-02 ; 2.71
0.0128
When I try to minimize the system, with grompp -f minimizado.mdp -c
final_system.gro -p final_system.top -o minimizado.tpr I find 2 warnings:
WARNING 1 [file final_system.top, line 19]:
Overriding atomtype c
WARNING 2 [file final_system.top, line 20]:
Overriding atomtype o
It is like it is not distinguing the capitals for amber and non-capitals for
gaff. Does anybody know which can be the cause of these warnings?
Thank you very much,
Rebeca Garcia
University of Oxford
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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