Hi everyone,
I have one simple question. I don't know is there any different between OPLS-AA
forcefield and OPLS-AA/L forcefield? I think these are different but when I use
pdb2gmx tool there is no OPLS-AA forcefield to choose.
Thank you
you zou wrote:
Hi everyone,
I have one simple question. I don't know is there any different
between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these are
different but when I use pdb2gmx tool there is no OPLS-AA forcefield to
choose.
There is no difference. The presence of /L
Justin A. Lemkul skrev:
you zou wrote:
Hi everyone,
I have one simple question. I don't know is there any different
between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these
are different but when I use pdb2gmx tool there is no OPLS-AA
forcefield to choose.
There is no
Erik Marklund wrote:
Justin A. Lemkul skrev:
you zou wrote:
Hi everyone,
I have one simple question. I don't know is there any different
between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these
are different but when I use pdb2gmx tool there is no OPLS-AA
forcefield to
Dear All,
I am trying to use the OPLS-AA force field to model some imidazole
containing compounds. I've noticed that imidazole units are referenced in
the ffoplsaa.atp file as the following:
opls_557 14.00670 ; N1 in imidazole
opls_558 12.01100 ; C2 in imidazole
opls_559 14.00670 ;
Jacob Harvey wrote:
Dear All,
I am trying to use the OPLS-AA force field to model some imidazole
containing compounds. I've noticed that imidazole units are referenced
in the ffoplsaa.atp file as the following:
opls_557 14.00670 ; N1 in imidazole
opls_558 12.01100 ; C2 in
Thank you for your help Justin. I have corrected my naming problem in the
pdb file. However, I am still getting errors. It does not seem to recognize
the residues. BUT I dont actually have residues in my system, because I am
not modeling a protein. So I am not sure what to put in the residue name
Jacob Harvey wrote:
Thank you for your help Justin. I have corrected my naming problem in
the pdb file. However, I am still getting errors. It does not seem to
recognize the residues. BUT I dont actually have residues in my
system, because I am not modeling a protein. So I am not sure what
Jacob Harvey wrote:
Justin,
How do I go about running topolgen on a linux system? There doesn't seem
to be instructions for use, but I'm not familiar with perl scripts. Also
I'd just like to say thank you for all your help. You've been really
good with responding to my e-mail. I know that
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