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.
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Hi
I can't see which commands you typed. Your second try "/bin/sh: 1: -i: not
found" means that you $PATH is not properly setup for Amber Tools. And if
you using open babel, it has to be your $PATH as well.
For the first case, it's all about which structure you were trying to run.
>From the pdbs
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 |
=
Hi there,
You said ACPYPE didn't work… Can you give details? Have you try with GAFF
first? If you don't mind, can you post me your molecule in private email?
Thanks,
Alan
On 9 July 2013 22:34, Melchor S. wrote:
> Sorry for the misunderstanding. I should had explained it better.
>
> I know th
On 7/9/13 5:34 PM, Melchor S. wrote:
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. Antecha
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
On 7/9/13 11:23 AM, Melchor S. wrote:
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 o
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
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
On 7/8/13 7:00 AM, Melchor S. wrote:
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.
There are a lot of variables at play here that you haven't described (Gromacs
version, pdb2gmx comm
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.
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