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<div style="DIRECTION: ltr" id="divRpF517226"><font color="#000000" size="2" face="Tahoma"><b>From:</b> Shima Arasteh [shima_arasteh2001@yahoo.com]<br>
<b>Sent:</b> Thursday, April 12, 2012 4:53 PM<br>
<b>To:</b> Marzinek, Jan<br>
<b>Subject:</b> Re: [gmx-users] Gromos87<br>
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<div><span>Dear Jan,</span></div>
<div><span>I downloaded the file and put it in my working space but does not appear in my force filed selections? How come?</span></div>
<div><span>What's wrong with it?</span></div>
<div><br>
<span></span></div>
<div><span>Cheers,</span></div>
<div><span>Shima<br>
</span></div>
<div> </div>
<div> </div>
<div>You should have downloaded not a single file but the whole force field which is a folder and the copy it to the directory you working in. As Felix mentioned it could be number:</div>
<div>17: [DEPRECATED] Gromacs force field (see manual)<br>
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<div>so you do not have to download it. Ensure this is a version you need.</div>
<div> </div>
<div>Jan<br>
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<b><span style="FONT-WEIGHT: bold">From:</span></b> "Marzinek, Jan" <j.marzinek10@imperial.ac.uk><br>
<b><span style="FONT-WEIGHT: bold">To:</span></b> Shima Arasteh <shima_arasteh2001@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org>
<br>
<b><span style="FONT-WEIGHT: bold">Sent:</span></b> Thursday, April 12, 2012 7:42 PM<br>
<b><span style="FONT-WEIGHT: bold">Subject:</span></b> RE: [gmx-users] Gromos87<br>
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<div style="DIRECTION: ltr" id="yiv6237076divRpF782976"><font color="#000000" size="2" face="Tahoma"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of Shima Arasteh [shima_arasteh2001@yahoo.com]<br>
<b>Sent:</b> Thursday, April 12, 2012 4:05 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] Gromos87<br>
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<div>Dear friends,</div>
<div><br>
</div>
<div>I'd like to use gormos87 force field in my simulation. Which force field am I supposed to select?</div>
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</div>
<div> 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)<br>
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)<br>
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)<br>
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)<br>
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)<br>
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)<br>
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)<br>
8: CHARMM27 all-atom force field (with CMAP) - version 2.0<br>
9: GROMOS96 43a1 force field<br>
10: GROMOS96 43a2 force field (improved alkane dihedrals)<br>
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br>
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)<br>
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)<br>
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br>
15: [DEPRECATED] Encad all-atom force field, using full solvent charges<br>
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges<br>
17: [DEPRECATED] Gromacs force field (see manual)<br>
18: [DEPRECATED] Gromacs force field with hydrogens for NMR</div>
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<div>Thanks in advance,</div>
<div>Shima</div>
<div> </div>
<div> </div>
<div>No clue why do you want to use this force field which is an old version. Would you like to reproduce some results?
</div>
<div>Download it and copy to your folder where you use pdb2gmx. It will appear as the first option then.</div>
<div> </div>
<div>Jan<br>
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