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Thank you very much, Alan.<BR>
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_.<BR>
Best wishes,<BR>
Rebeca.<BR> <BR>
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From: alanwilter@gmail.com<BR>Date: Thu, 4 Jun 2009 22:19:30 +0100<BR>To: gmx-users@gromacs.org<BR>Subject: [gmx-users] Re: goverrriding problem<BR><BR>
<DIV class=EC_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 style="BORDER-LEFT: #ccc 1px solid; PADDING-LEFT: 1ex" class=EC_gmail_quote><BR>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><br /><hr />Comparte tus fotos con tus amigos. Más fácil con <a href='http://download.live.com' target='_new'>Windows Live</a></body>
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