[gmx-users] unscribe

Dear Sir,   I want to unscribe there emails, thank. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- 12年1月12日，周四, Mark Abraham 写道： 发件人: Mark Abraham 主题

[gmx-users] (no subject)

Dear all, When I try to install gromacs-4.5.5 on my centos system, I meet trouble. I installed fftw-3.3.2 and then install gromacs-4.5.5. When I type /.configure command, I got the error information: checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-g

[gmx-users] grompp error

Dear Sir'   When I ran the grompp as following   grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr   a error information appeared:     Program grompp, VERSION 3.3.1 Source code file: readir.c, line: 789 Fatal error: Group Ptotein not found in indexfile Maybe you have non-default goups in your

Re: [gmx-users] grompp error

日,周五,下午4:21 The most reasonable thing is that there is a typo in your .mdp or in your .top files. Check where you've written "Ptotein" instead of Protein On 11/25/11 4:09 PM, yp sun wrote: Dear Sir'   When I ran the grompp as following   grompp -v -f md.mdp -c pr.gro

Re: [gmx-users] grompp error

written "Ptotein" instead of Protein On 11/25/11 4:09 PM, yp sun wrote: Dear Sir'   When I ran the grompp as following   grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr   a error information appeared:     Program grompp, VERSION 3.3.1 Source code file: readir.c, line:

Re: [gmx-users] .top to .itp file conversion

I think by running pdb2gmx you can get .itp file. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china --- 11年11月28日，周一, David van der Spoel 写道： 发件人: David van

[gmx-users] Atom not found in residue while adding hydrogens

Dear Sir,   When I run pdb2gmx, I encounter the following error information: Program pdb2gmx, VERSION 3.3.1 Source code file: genhydro.c, line: 304 Fatal error: Atom CB not found in residue ASP223 while adding hydrogens What should I do? Yeping Sun CAS Key Laboratory of Pathogenic Microbiology

Re: [gmx-users] Atom not found in residue while adding hydrogens

写道： 发件人: Mark Abraham 主题: Re: [gmx-users] Atom not found in residue while adding hydrogens 收件人: "Discussion list for GROMACS users" 日期: 2011年11月28日,周一,下午7:25 On 28/11/2011 10:13 PM, yp sun wrote: Dear Sir,   When I run pdb2gmx, I encounter the following error information: P

回复： [gmx-users] No such moleculetype Na

The name of ion is different when using different force field You can check which field force you use and find out how Na and Cl ion is written in this force field. Yeping Sun CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 B

[gmx-users] analysis the results of melocular dynamics simulation

Dear Sir,   I finished my simulation with gromacs, but whatever orders I use to analysize the results, I always get errors. For example, when I type: g_density -f  md.trr It returns: Program g_density, VERSION 3.3.1 Source code file: gmxfio.c, line: 706 Can not open file: topol.tpr When I type

[gmx-users] select groups in g_rms

Dear Sir,   When I run g_rms -s md.tpr -f md.trr -o rmsd.xvg, the program requires me selecting a group twice as following:   g_rms -s md.tpr -f md.trr -o rmsd.xvg后, 程序两次要求选结构组,如下: Reading file md.tpr, VERSION 3.3.1 (single precision) Reading file md.tpr, VERSION 3.3.1 (single precision) Select