[gmx-users] amber force field in gromacs

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

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

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

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

Dear Leila, Consider reading all about ACPYPI at acpypi.googlecode.com, specially the wiki pages. Although you may not be interested in topology generation for ligands, there's there important information about how to run amber force fields in Gromacs environment. And review carefully your ffambe

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

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

Re: [gmx-users] access code for qmmm

Hi, I saw web page for ORCA, and I saw an access code for QM/MM ORCA interface, but I do'nt know, how do I can install. please guide me.  Farzad Molani, Ph.D Student, Department of Theoretical Chemistry and Biochemistry, K. N. Toosi University of Technology, Tehran, Iran. Tel.: 009821 2306 4280

Re: [gmx-users] access code for qmmm

Farzad Molani wrote: Hi, I saw web page for ORCA, and I saw an access code for QM/MM ORCA interface, but I do'nt know, how do I can install. please guide me. What's the problem? Google for the home pages and follow the instructions there. Mark --- On *Tue, 11/17/09, ilona.bal...@bioquant.

[gmx-users] 4. Re: access code for qmmm (Mark Abraham)

You need a newer version to run ORCA: 1016:42git clone git://git.gromacs.org/gromacs 1116:44cd gromacs/ 1216:44git branch --track qmmm origin/qmmm 1316:44git checkout qmmm 1416:44git pull Gerrit On 21 Nov 2009, at 14:16, gmx-users-requ...

RE: [gmx-users] Pushing MD further

There exists a (non-official) TEE-REX prototype for GMX 4 which allows full parallelization of each TEE-REX copy. Just contact ckut...@gwdg.de for more information. Marcus > I would also add that you could also use TEE-REX which overcomes some of > the problems associated with normal REMD on lar

Re: [gmx-users] access code for qmmm

Hi, I want to couple gromacs and orca. I saw ORCA interface is written by Gerrit Groenhof. How do I install ORCA interface with ORCA and GROMACS?   Farzad Molani, Ph.D Student, Department of Theoretical Chemistry and Biochemistry, K. N. Toosi University of Technology, Tehran, Iran. Tel.: 009821 2

Re: [gmx-users] 4. Re: access code for qmmm (Mark Abraham)

I have gromacs4.0. Farzad Molani, Ph.D Student, Department of Theoretical Chemistry and Biochemistry, K. N. Toosi University of Technology, Tehran, Iran. Tel.: 009821 2306 4280 Fax: 009821 2285 3650 Web: http://www.kntu.ac.ir --- On Sat, 11/21/09, Gerrit Groenhof wrote: From: Gerrit Groenhof

Re: [gmx-users] 4. Re: access code for qmmm

Hi Dr.Greonhof, Thanks for your reply. I am using gromacs 3.3 and gromacs 4.0. I did'nt undrestand about your advice. please help me clearly. Thanks in advance. Farzad Molani, Ph.D Student, Department of Theoretical Chemistry and Biochemistry, K. N. Toosi University of Technology, Tehran, Iran. T

Re: [gmx-users] 4. Re: access code for qmmm (Mark Abraham)

Hi Dr.Greonhof, Thanks for your reply. I am using gromacs 3.3 and gromacs 4.0. I did'nt undrestand about your advice. please help me clearly. Thanks in advance. Farzad Molani, Ph.D Student, Department of Theoretical Chemistry and Biochemistry, K. N. Toosi University of Technology, Tehran, Iran. T

Re: [gmx-users] 4. Re: access code for qmmm

Farzad Molani wrote: Hi Dr.Greonhof, Thanks for your reply. I am using gromacs 3.3 and gromacs 4.0. I did'nt undrestand about your advice. please help me clearly. I don't know what can be more clear than exact commands. You need to access the newest version of the development code. See he

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

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] 4. Re: access code for qmmm (Mark Abraham)

Farzad Molani wrote: I have gromacs4.0. At the very least that should be upgraded to 4.0.5. There are many significant known bugs in 4.0. Also, please have a read of the tips on mailing list etiquette here, http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette especially the

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

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

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