________________________________ From: Shima Arasteh [shima_arasteh2...@yahoo.com] Sent: Thursday, April 12, 2012 4:53 PM To: Marzinek, Jan Subject: Re: [gmx-users] Gromos87 Dear Jan, I downloaded the file and put it in my working space but does not appear in my force filed selections? How come? What's wrong with it? Cheers, Shima 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: 17: [DEPRECATED] Gromacs force field (see manual) so you do not have to download it. Ensure this is a version you need. Jan ________________________________ From: "Marzinek, Jan" <j.marzine...@imperial.ac.uk> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Thursday, April 12, 2012 7:42 PM Subject: RE: [gmx-users] Gromos87 ________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Shima Arasteh [shima_arasteh2...@yahoo.com] Sent: Thursday, April 12, 2012 4:05 PM To: Discussion list for GROMACS users Subject: [gmx-users] Gromos87 Dear friends, I'd like to use gormos87 force field in my simulation. Which force field am I supposed to select? 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (with CMAP) - version 2.0 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 15: [DEPRECATED] Encad all-atom force field, using full solvent charges 16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges 17: [DEPRECATED] Gromacs force field (see manual) 18: [DEPRECATED] Gromacs force field with hydrogens for NMR Thanks in advance, Shima No clue why do you want to use this force field which is an old version. Would you like to reproduce some results? Download it and copy to your folder where you use pdb2gmx. It will appear as the first option then. Jan
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