<div class="gmail_quote"><div>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.</div><div><br></div><div>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?).</div>
<div><br></div><div>Otherwise do it yourself by making c_ and o_ and the overriding warn will be off.</div><div><br></div><div>Cheers,</div><div>Alan</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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Message: 7<br>
Date: Thu, 4 Jun 2009 20:55:52 +0000<br>
From: Rebeca Garc?a Fandi?o <<a href="mailto:regafan@hotmail.com">regafan@hotmail.com</a>><br>
Subject: [gmx-users] overrriding problem<br>
To: <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <BAY142-W269F0995D7F3B4890E330DB74B0@phx.gbl><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
<br>
Hi,<br>
I am doing a simulation combining amber and Gaff force field (for dopc lipids), this is the first part of my topology file:<br>
<br>
; UNK_GMX.top created by acpypi on Thu Jun 4 22:06:03 2009<br>
<br>
[ defaults ]<br>
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
1 2 yes 0.5 0.8333<br>
<br>
[ atomtypes ]<br>
;name bond_type mass charge ptype sigma epsilon Amb<br>
CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860<br>
CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094<br>
C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860<br>
HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000<br>
O O 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100<br>
OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104<br>
c3 c3 12.0100 -0.12654 A 3.399676e-01 4.577296e-01 ; 1.91 0.1094<br>
hc hc 1.0080 0.02245 A 2.649538e-01 6.568880e-02 ; 1.49 0.0157<br>
c2 c2 12.0100 -0.15458 A 3.399676e-01 3.598240e-01 ; 1.91 0.0860<br>
ha ha 1.0080 0.11146 A 2.599647e-01 6.276000e-02 ; 1.46 0.0150<br>
c c 12.0100 0.44800 A 3.399676e-01 3.598240e-01 ; 1.91 0.0860<br>
o o 16.0000 -0.47180 A 2.959927e-01 8.786400e-01 ; 1.66 0.2100<br>
os os 16.0000 -0.15429 A 3.000018e-01 7.112800e-01 ; 1.68 0.1700<br>
h1 h1 1.0080 0.16551 A 2.471358e-01 6.568880e-02 ; 1.39 0.0157<br>
p5 p5 30.9700 1.14364 A 3.741781e-01 8.368000e-01 ; 2.10 0.2000<br>
n4 n4 14.0100 0.01626 A 3.250004e-01 7.112800e-01 ; 1.82 0.1700<br>
hx hx 1.0080 0.08244 A 1.959981e-01 6.568880e-02 ; 1.10 0.0157<br>
OW OW 0.00000 0.00000 A 3.16572e-01 6.49775e-01 ; 1.78 0.1553<br>
HW HW 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000<br>
Na Na 0.00000 0.00000 A 2.15954e-01 1.47545e+00 ; 1.21 0.3526<br>
Cl Cl 0.00000 0.00000 A 4.83045e-01 5.34924e-02 ; 2.71 0.0128<br>
<br>
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:<br>
<br>
WARNING 1 [file final_system.top, line 19]:<br>
Overriding atomtype c<br>
WARNING 2 [file final_system.top, line 20]:<br>
Overriding atomtype o<br>
<br>
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?<br>
<br>
Thank you very much,<br>
<br>
Rebeca Garcia<br>
University of Oxford<br></blockquote></div><br>-- <br>Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>Department of Biochemistry, University of Cambridge.<br>80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>>><a href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>