Re: [gmx-users] gmx-user : problem with coordinate number

2012-08-02 Thread Mark Abraham
On 3/08/2012 1:51 PM, Nur Syafiqah Abdul Ghani wrote: Dear All, My project is about protein simulation in mix-solvent. At first I used pdb2gmx command then editconf for stting up my box. My co-solvent I creat it from PRTDRG server to get pdb and itp file. 1. I get the name of the file is DRG.I

[gmx-users] gmx-user : problem with coordinate number

2012-08-02 Thread Nur Syafiqah Abdul Ghani
Dear All, My project is about protein simulation in mix-solvent. At first I used pdb2gmx command then editconf for stting up my box. My co-solvent I creat it from PRTDRG server to get pdb and itp file. 1. I get the name of the file is DRG.ITP with capital letter.Then i change it with new name w

RE: [gmx-users] [gmx-user]Error by pdb2gmx

2010-05-27 Thread Dallas B. Warren
; To: gmx-users@gromacs.org > Subject: [gmx-users] [gmx-user]Error by pdb2gmx > > Dear Editors: > I used gromacs version 4.0.7. I update ffG45a3.rtp to include my > molecule with its rtp in the attached file DRG.txt.And the pdb file of > my molecule is mol.txt and also attached. When I used

[gmx-users] [gmx-user]Error by pdb2gmx

2010-05-27 Thread 佘安奇
Dear Editors: I used gromacs version 4.0.7. I update ffG45a3.rtp to include my molecule with its rtp in the attached file DRG.txt.And the pdb file of my molecule is mol.txt and also attached. When I used the following command,there is an error! "pdb2gmx_mpi -ff G45a3 -f iso-C16.PDB" Opening l

Re: [gmx-users] [gmx-user]Error by pdb2gmx

2010-05-18 Thread Mark Abraham
- Original Message - From: 佘安奇   Date: Wednesday, May 19, 2010 16:17 Subject: [gmx-users] [gmx-user]Error by pdb2gmx To: gmx-users@gromacs.org --- | > Dear Yanmei Song： > I used gromacs version 3.3.1. I update ffG45a3.

[gmx-users] [gmx-user]Error by pdb2gmx

2010-05-18 Thread 佘安奇
Dear Yanmei Song： I used gromacs version 3.3.1. I update ffG45a3.rtp to include my molecule. When I run pdb2gmx using my molecules with the command:   "pdb2gmx -f min_C16.pdb -o C16.pdb -p topol.top -ff G45a3"    I got the error message: "  Opening library file ffG45a3.rtp   Opening library file 

Re: [gmx-users] gmx user

2009-11-03 Thread Justin A. Lemkul
pawan raghav wrote: Hello Users, I am trying to install gromacs on windows and find lot of problems. First I have installed Cygwin with gcc, gdb and make packages. Then FFTW-3.2.2 and configure it but when I used make and make install commands but some directories leave as it is. When conf

[gmx-users] gmx user

2009-11-03 Thread pawan raghav
Hello Users, I am trying to install gromacs on windows and find lot of problems. First I have installed Cygwin with gcc, gdb and make packages. Then FFTW-3.2.2 and configure it but when I used make and make install commands but some directories leave as it is. When configure gromacs-4.0.5 then it

Re: [gmx-users] gmx user

2009-11-01 Thread Mark Abraham
pawan raghav wrote: Dear all, I am a new user of GROMACS and suffering from severe problem about fftw-3.2.2 installation. Actually I have installed cygwin on windows XP with gcc, gdb, and make packages rest all are leaved default. Now when I have used configure command then it would give las

[gmx-users] gmx user

2009-11-01 Thread pawan raghav
Dear all, I am a new user of GROMACS and suffering from severe problem about fftw-3.2.2 installation. Actually I have installed cygwin on windows XP with gcc, gdb, and make packages rest all are leaved default. Now when I have used configure command then it would give last line as config.status: