[gmx-users] Gromos87

[Marzinek, Jan]

________________________________
From: Shima Arasteh [shima_arasteh2001 at 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.marzinek10 at imperial.ac.uk>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thursday, April 12, 2012 7:42 PM
Subject: RE: [gmx-users] Gromos87

________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Shima Arasteh [shima_arasteh2001 at 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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