Maria Hamilton wrote:
Hi Justin
If I want to have Decane.itp file in Amber forcefield for TIP4P-EW what
should I do?
In the future, please make sure to:
1. copy only the relevant portion of the digest
2. change the subject line to attract attention
To answer your question, the link I provi
Maria Hamilton wrote:
Hi all friends
If I want to use tip4pew model for water from Amber forcefield, can I
use itp files in PRODRG site for the other components?
PRODRG topologies are (supposedly) compatible with Gromos force fields, but
TIP4P-EW is not implemented for any of these param
In latest version of gromacs (4.5.4 or earlier)
The amber force fields were provided.
--
Best Regards,
lina
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Hi all friends
If I want to use tip4pew model for water from Amber forcefield, can I use
itp files in PRODRG site for the other components?
Thanks
Regards
Maria
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This kind of problems can occur if you were restraining atom positions and using
pressure coupling.
Best regards
Lucio.
Lucio Ricardo Montero Valenzuela
PhD Student
Laboratorio del Dr. Federico Sánchez
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cu
> servaas skrev:
> >> Message: 4
> >> Date: Tue, 1 Dec 2009 13:56:21 +
> >> From: Alan
> >> Subject: [gmx-users] Re: amber force field in Gromacs
> >> To: gmx-users@gromacs.org
> >> Message-ID:
> >>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> Dear Servaas,
> >>
> >> I've b
servaas skrev:
Message: 4
Date: Tue, 1 Dec 2009 13:56:21 +
From: Alan
Subject: [gmx-users] Re: amber force field in Gromacs
To: gmx-users@gromacs.org
Message-ID:
Content-Type: text/plain; charset=UTF-8
Dear Servaas,
I've been following your thread. I am the developer of acpypi and
> Message: 4
> Date: Tue, 1 Dec 2009 13:56:21 +
> From: Alan
> Subject: [gmx-users] Re: amber force field in Gromacs
> To: gmx-users@gromacs.org
> Message-ID:
>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Servaas,
>
> I've been following your thread. I am the developer of ac
servaas wrote:
Hello,
I tried using the amber force field in GROMACS. I proceeded as follows:
Determined my parameters with RED/ANTECHAMBER/tleap converted them with amb2gmx.pl
(or with acpypi, problem is the same) to gromacs coordinate and topology files. It concerns a modified nucleotide. I m
Hello,
I tried using the amber force field in GROMACS. I proceeded as follows:
Determined my parameters with RED/ANTECHAMBER/tleap converted them with
amb2gmx.pl
(or with acpypi, problem is the same) to gromacs coordinate and topology files.
It concerns a modified nucleotide. I minimized with s
Hi,
Sorry for my mistake before, column 17 should be alternative location code,
not blank.
Good luck
Terry
2009/11/21 leila karami
> Hi
>
> I used amber03 force field in gromacs to study pr-dna interaction.
> I compare my pdb file and ffamber03.rtp file.
> I should correct my pdb file to tal
Hi Leila,
I think it is a pdb format problem. According to pdb convention, column 17
should be left blank and columns 18-20 are used for residue name.
Please check your pdb format first. Good luck.
Terry
2009/11/21 leila karami
> Hi
>
> I used amber03 force field in gromacs to study pr-dna in
On Sat, November 21, 2009 at 2:36:08 AM, leila karami
wrote:
> I used amber03 force field in gromacs to study pr-dna interaction.
> I compare my pdb file and ffamber03.rtp file.
> I should correct my pdb file to tally with rtp file. N-terminal (NUMBER 1)
> and C-terminal
> (NUMBER 70) of my
leila karami wrote:
dear Mark
your opinion is right [residue number 1 is NGLY in pdb file but residue
number 1 is GLY in warning].
howbeit, what work should I do?
Can you post an actual copy-and-paste snippet from your .pdb file? So far, you
have shown a few re-typed parts of lines t
dear Mark
your opinion is right [residue number 1 is NGLY in pdb file but residue
number 1 is GLY in warning].
howbeit, what work should I do?
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leila karami wrote:
dear Mark
my command is: pdb2gmx -f c.pdb -p c.top -o c.gro .
I think what I'm doing is clear. also there is GLY 1 :
pdb file of GLY 1
1 N NGLY 1
2 CA NGLY 1
3
dear Mark
my command is: pdb2gmx -f c.pdb -p c.top -o c.gro .
I think what I'm doing is clear. also there is GLY 1 :
pdb file of GLY 1
1 N NGLY 1
2 CA NGLY 1
3 C NGLY 1
4 O NGLY 1
5 1H NGLY 1
6 2HA NGLY 1
7 2H NGLY 1
8 3H NGLY 1
9 1HA NGLY 1
rtp file of GLY 1
[ NGLY ]
[ at
leila karami wrote:
Hi
I used amber03 force field in gromacs to study pr-dna interaction.
I compare my pdb file and ffamber03.rtp file.
I should correct my pdb file to tally with rtp file. N-terminal (NUMBER
1) and C-terminal (NUMBER 70) of my protein is GLY.
pdb file and rtp file relating to
Hi
I used amber03 force field in gromacs to study pr-dna interaction.
I compare my pdb file and ffamber03.rtp file.
I should correct my pdb file to tally with rtp file. N-terminal (NUMBER 1)
and C-terminal (NUMBER 70) of my protein is GLY.
pdb file and rtp file relating to gly1 and gly70 are place
Read the documentation on the site where you got the ffamber ports:
http://chemistry.csulb.edu/ffamber/index.html#usage
The Amber force fields are particular about residue nomenclature.
-Justin
Quoting Liu Shiyong <[EMAIL PROTECTED]>:
> Hi,
>
> I install amber force filed according to source
Hi,
I install amber force filed according to source:
http://chemistry.csulb.edu/ffamber/index.html
But , I run pdb2gmx, I got a problem.
Program pdb2gmx, VERSION 3.3.1
pdb2gmx -ignh -ff amber99 -f r-l_1.pdb
Opening library file /export/apps/gromacs-3.3.1-Amber
/share/gromacs/top//ffamber99
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