[gmx-users] Acetyl capping and Range checking error

tem is properly energy-minimized and that the potential energy seems reasonable before trying again. Variable ci has value -2147483648. It should have been within [ 0 .. 125 ] How could I solve the problem? Should I modify something else other than the pdb? Thanks in advance

RE: [gmx-users] Proline on OPLSSaa

he bonds, angles and dihedrals in the .rtp file is not enough. You'll > have to assign parameters to them. Check the entries (notably PRO and > ACE) in the .rtp file of your choice... > > Cheers, > > Tsjerk > > On Feb 11, 2008 12:02 AM, Mark Abraham <[EMAIL PROT

[gmx-users] Proline on OPLSSaa

e #ifdef POSRES #include "posre.itp" #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name %E in water [ molecules ] ; Compound#mols Protein 1 SOL 2390 Can somebody pelase tell what I'm doing wrong? Thanks in advanc

[gmx-users] chloroform - oplsaa

Hi all, I'm trying to run a simulation of a phenol in chloroform with the oplsaa forcefield. I've downloaded the chloroform box from gromacs and added the files to the top folder. Everything is fine till I run grompp which says: Fatal error: Invalid order for directive atomtypes, file ""/usr/l

RE: [gmx-users] ffamber_chcl3.gro

So this means that for me it's impossible to run the simulation of a phenol in a box of chloroform with ffamber99? > Date: Tue, 4 Dec 2007 12:01:01 -0500 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] ffamber_chcl3.gro > > Quotin

RE: [gmx-users] ffamber_chcl3.gro

Hi all, I have to run a simulation in a box of chloroform. I've found a chcl3.itp and a chcl3_box.gro files but I'm using ffamber99 forcefield. Is it possible to modify someway the two files above? Where can I find the informations to do that? Thanks in advance

[gmx-users] Chloroform

Hi all! I've to run a simulation in a box filled with chloroform. I'm using GROMACS with amber99 force field but I'm a beginner and I have no idea about how to set up the box or where to find the topology. Thanks for your help _ Or

[gmx-users] Fatal error

Dear all, I was running grompp with a symple phenol and I get this error message Fatal error: [ file "/usr/share/gromacs/top/spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) I didn't make any change in spc.itp file so that sounds a bit strange. Does anyone have an