Re: [gmx-users] amber convert gromacs input files

2010-12-24 Thread Alan Wilter Sousa da Silva
Have a good look in acpype, specially its wiki. There you'll see that acpype is totally new code and among other things it covers amb2gmx.pl and solves several of its drawbacks. It's not perfect though but for a system created in tleap, the project is likely to be completed converted to gmx. Alan

Re: [gmx-users] amber convert gromacs input files

2010-12-23 Thread Mark Abraham
On 23/12/2010 6:02 PM, gromacs564 wrote: Hi , I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) ,but cannot converted this amber files to gromacs files format. Can anyone help me to convert this

Re: [gmx-users] amber convert gromacs input files

2010-12-23 Thread Alan Wilter Sousa da Silva
Have a look at acpype.googlecode.com Alan 2010/12/23 gromacs564 gromacs...@126.com Hi , I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) , but cannot converted this amber files to gromacs files format.

Re: [gmx-users] amber convert gromacs input files

2010-12-23 Thread Oliver Grant
Hi, Not sure exactly what you plan to simulate but here are a couple of potential pitfalls: Does acpype call amb2gmx.pl or is it new code that converts? If it is a amb2gmx.pl call I'd check the torsions on the NAc group if you have one. They didn't get translated when I used it. When using

[gmx-users] amber convert gromacs input files

2010-12-22 Thread gromacs564
Hi , I have obtained some files(.top,.crd,.pdb) about disaccharide via glycam web(they are glycam06 force field,included in AMBER) , but cannot converted this amber files to gromacs files format. Can anyone help me to convert this (amber) files to gromacs input files(top or