[gmx-users] Re: Problem with Amber99SB-ILDN ff

Hi, This is more or less that I was thinking after look carefully all the errors. Thank you for your answer and your time. Melchor S. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-Amber99SB-ILDN-ff-tp5009641p5010029.html Sent from the GROMACS Users Forum

[gmx-users] Re: Problem with Amber99SB-ILDN ff

Hi again, I can give more details about acpype error. This is the error that I obtained, === | ACPYPE: AnteChamber PYthon Parser interfacE v. 2012-09-13 14:55:47Z Rev: 389 (c) 2012 AWSdS | =

[gmx-users] Re: Problem with Amber99SB-ILDN ff

Sorry for the misunderstanding. I should had explained it better. I know that is a zwitterionic residue, I have run several simulations with the same PDB and with other forcefields. ACPYPE does not work, I tried it yesterday, but I have to check it. Antechamber I don't know, I have to try it. Als

[gmx-users] Re: Problem with Amber99SB-ILDN ff

I am using gromacs 4.5.5, I didn't tell you yesterday. I have been tried a lot of things, but without any success. One of that I think has to work fine, is with the NGLU nomenclature, but when I use it, I obtain this There is a dangling bond at at least one of the terminal ends and the force fiel

[gmx-users] Re: Problem with Amber99SB-ILDN ff

For sure there are a lot of variable playing here, I only ask about the MET for curiosity, because I am a beginner in this kind of things we can say... I do : pdb2gmx -f pdb.pdb -p pdb.top -o pdb.gro -water spc -his -ter -posrefc 1. I don't specify nothing as separate chains or so on. I wil

[gmx-users] Re: Problem with Amber99SB-ILDN ff

Ok, I will try it. Thank you. But when a chain starts with MET why this nomenclature is not needed? Because with MET works fine like any other forcefield. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-Amber99SB-ILDN-ff-tp5009641p5009643.html Sent from the GROMA

[gmx-users] Problem with Amber99SB-ILDN ff

I am trying to create the gromacs topology and gro file, using pdb2gmx, with the Amber99SB-ILDN ff. The problem is that my protein has two chains, but the second one, is a one residue chain, that contains a GLU. When I try it I obtain: Fatal error: In the chosen force field there is no residue

[gmx-users] Problem creating the gro file with Amber

Hi all, I am trying to create the gromacs topology and gro file, using pdb2gmx, with the Amber99SB-ILDN ff. The problem is that my protein has two chains, but the second one, is a one residue chain, that contains a GLU. When I try it I obtain: Fatal error: In the chosen force field there is no

[gmx-users] Re: Problem calculating RMSD with gromos

s are very similar, in principle, as I can see in VMD and so on, but for sure I will try your suggestions. Cheers, Melchor S. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-calculating-RMSD-with-gromos-tp5009494p5009500.html Sent from the GROMACS Users Forum mailing

[gmx-users] Re: Problem calculating RMSD with gromos

png> cheers, Melchor S. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-calculating-RMSD-with-gromos-tp5009494p5009497.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Problem calculating RMSD with gromos

I run the "production" molecular dynamics starting from the SA trajectory. For analize the trajectory succesfully, I use the pbc nojump and fit rot+trans options. Melchor S. -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-calculating-RMSD-with-gromos-tp500949