Re: [gmx-users] amber force field in Gromacs

2009-12-04 Thread Lucio Ricardo Montero Valenzuela
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

[gmx-users] amber force field in Gromacs

2009-12-02 Thread servaas
> 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

Re: [gmx-users] amber force field in Gromacs

2009-12-01 Thread Erik Marklund
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

[gmx-users] amber force field in Gromacs

2009-12-01 Thread servaas
> 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

Re: [gmx-users] amber force field in Gromacs

2009-11-30 Thread Mark Abraham
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

[gmx-users] amber force field in Gromacs

2009-11-30 Thread servaas
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

Re: [gmx-users] amber force field in gromacs

2009-11-21 Thread Terry
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

Re: [gmx-users] amber force field in gromacs

2009-11-21 Thread Terry
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

Re: [gmx-users] amber force field in gromacs

2009-11-21 Thread Bruce D. Ray
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

Re: [gmx-users] amber force field in gromacs

2009-11-21 Thread Justin A. Lemkul
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

[gmx-users] amber force field in gromacs

2009-11-21 Thread leila karami
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? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

Re: [gmx-users] amber force field in gromacs

2009-11-21 Thread Mark Abraham
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

[gmx-users] amber force field in gromacs

2009-11-21 Thread leila karami
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

Re: [gmx-users] amber force field in gromacs

2009-11-20 Thread Mark Abraham
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

[gmx-users] amber force field in gromacs

2009-11-20 Thread 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 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