On 2/5/13 2:10 AM, az kalsom wrote:
hi,
i wanted to say i am not able to make acpype for me, i am following the
tutorial , http://code.google.com/p/acpype/wiki/HowToUse
but i am still geeting the error that this comand is not found
anybody please help me
It's just a Python script, so you c
On 1/29/13 2:44 PM, az kalsom wrote:
hi,
when i run the comand
acpype -i lig.pdb
it says command not found
even i have installed latest version of groamcs,
what to do ?
acpype is not a Gromacs program; it is an accessory that someone else developed.
You will have to install it separate
hi,
when i run the comand
acpype -i lig.pdb
it says command not found
even i have installed latest version of groamcs,
what to do ?
regards
kalsoom
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Hi Thales,
Amber 1.5? You mean Amber12 and ambertools12?
I haven't test with them yet, but it would help me if you run in the debug
mode and post the output here for me:
acpype -di proteinname.mol2 -c user
Thanks,
Alan
On 26 April 2012 19:02, Thales Kronenberger wrote:
> I configure Amber1
I configure Amber1.5 and installed the Acpype compatible (the tests went
pretty well)
BUT when I tried to submit my own job by the line
acpype -i proteinname.mol2 -c user
i got the message:
==
=
| ACPYPE
Kyle, can you send and pdb file so I can reproduce your issue?
Thanks,
Alan
On 24 February 2012 23:25, Kyle Greenway wrote:
>
> Hello,
>
> This email is directed mainly to Alan, who created Acpype.
>
> I've noticed that Acpype has assigned dihedral constants as 0.65084 for
> many dihedrals of
I will have a look coming Monday. Thanks for reporting that.
Alan
On 24 February 2012 23:25, Kyle Greenway wrote:
>
> Hello,
>
> This email is directed mainly to Alan, who created Acpype.
>
> I've noticed that Acpype has assigned dihedral constants as 0.65084 for
> many dihedrals of the form X
Hello,
This email is directed mainly to Alan, who created Acpype.
I've noticed that Acpype has assigned dihedral constants as 0.65084 for many
dihedrals of the form X -c3-n4-X, X -c3-c3-X, and others, in my generated
GROMACS .itp files. These dihedrals have values of 1.400 in the amber 99s
Indeed, if you do the other way:
0.65084/4.184 = 0.1 ~ 0.156
Alan
On 6 October 2011 08:17, Yun Shi wrote:
> Hi Alan,
>
> So is acpype using a conversion factor of 4.184 for dihedral force
> constant?
>
> I found some dihedral constants as 0.156 in the amber format, which should
> be 0.156
Hi Alan,
So is acpype using a conversion factor of 4.184 for dihedral force constant?
I found some dihedral constants as 0.156 in the amber format, which should
be 0.156*4.184=0.652704 in gromacs unit. However, acpype gave a force
constant of 0.65084 after conversion, which is slightly off. I won
Hi Yun,
ACPYPE is working fine. What happens here is I choose the reproduce the
exact values one sees in AMBER.
Now why GMX tip3p file choose a different value, I don't know.
Nevertheless, it's pretty simple to put whatever value you want there if you
think you need.
Alan
On 26 September 2011
Hi all,
I just noted that the tip3p water converted from amber format to gromacs
format is
[ moleculetype ]
; molname nrexcl ; TIP3P model
WAT 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 OW 1 WAT O 1 -0.834 16
Hi Liao,
Your python installation seems to be missing the datetime module, which is
very bizarre. Please verify your Python installation, you may have issues
with your PYTHONPATH.
Regards,
Alan
2011/4/12 fancy2012
> Hi GMX users,
> When I ran acpype.py on my computer, I got one error like th
ipn.mx; aldoseg...@gmail.com
=
--- El lun 11-abr-11, fancy2012 escribió:
De: fancy2012
Asunto: [gmx-users] Acpype error
A: "gmx-users"
Fecha: lunes, 11 de abril de 2011, 20:27
Hi GMX users,
When I ran acpype.py on my computer, I got one error lik
Hi GMX users,
When I ran acpype.py on my computer, I got one error like this:
File "./acpype.py", line 67, in
from datetime import datetime
ImportError: No module named datetime
I use Python-2.6.6, I do not know how this error happen, could someone help me
figure it out? Thanks very much in a
>>
>>
>> Date: Mon, 17 Jan 2011 06:47:35 +1100
>> From: Mark Abraham
>> Subject: Re: [gmx-users] ACPYPE download
>> To: Discussion list for GROMACS users
>> Message-ID: <4d334b57.7050...@anu.edu.au>
>> Content-Type: text/plain; charset=ISO-8
<mailto:mark.abra...@anu.edu.au>>
Subject: Re: [gmx-users] ACPYPE download
To: Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>>
Message-ID: <4d334b57.7050...@anu.edu.au
<mailto:4d334b57.7050...@anu.edu.au>>
Content-Type: text/plain; charset=ISO-8859-1; for
I did find this page and followed the instructions. But I can not download
it.
JH
Date: Mon, 17 Jan 2011 06:47:35 +1100
From: Mark Abraham
Subject: Re: [gmx-users] ACPYPE download
To: Discussion list for GROMACS users
Message-ID: <4d334b57.7050...@anu.edu.au>
Content-Type: text/plain; c
Go to
http://code.google.com/p/acpype/wiki/HowToUse
for instructions on installation of ACPYPE. There are also some very nice
acpype tutorials located at
http://code.google.com/p/acpype/w/list
Enjoy!
John
John E. Kerrigan, Ph.D.
Associate Director Bioinformatics
The Cancer Institute o
On 17/01/2011 5:05 AM, Jianhui Tian wrote:
Hi there,
I am trying to convert a AMBER XLEaP generated topology file of
Glycoprotein to GMX. The mailling list showed that ACPYPE should do
the work. However, I can not get the program following the
instructions on the wiki page. Is there anyone wh
Hi there,
I am trying to convert a AMBER XLEaP generated topology file of Glycoprotein
to GMX. The mailling list showed that ACPYPE should do the work. However, I
can not get the program following the instructions on the wiki page. Is
there anyone who has successful experience using ACPYPE and wou
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