[gmx-users] Distance restraint

Hi, I have a system with a protein and two different ligands. I'm trying to use distance restrain to hold the ligands inside the protein during a free energy calculation. If I use the distance restrains only between the protein and the first ligand I don't get any error, but if I introduce

[gmx-users] g_cluster questions

Hi all, I'm using this tool to cluter 2200 structures in this way: fitting on the backbone, rmsd calculated on key residues (10) of the Binding site. Now I created the correct group in the index file and using the g_cluster giving the trajectory as input i can only choose one group for fitting and

Re: [gmx-users] g_cluster questions

Hi, Try -nofit 2 okt 2007 kl. 09.28 skrev andrea carotti: Hi all, I'm using this tool to cluter 2200 structures in this way: fitting on the backbone, rmsd calculated on key residues (10) of the Binding site. Now I created the correct group in the index file and using the g_cluster giving the

[gmx-users] Nucleic Acid Simulations with Gromacs

Dear All, I want to start nucleic acid simulations. I am using gromacs3.3.1. But I could not find any mention of Nucleic Acids in any of the force-field provided by gromacs distro. So does it mean that one _can not_ simulate nucleic acids with gromacs. Has anyone tried? And if someone can

Re: [gmx-users] Nucleic Acid Simulations with Gromacs

the amber port from eric j sorin. On 10/2/2007 6:44 PM, Monika Sharma wrote: Dear All, I want to start nucleic acid simulations. I am using gromacs3.3.1. But I could not find any mention of Nucleic Acids in any of the force-field provided by gromacs distro. So does it mean that one _can not_

Re: [gmx-users] Nucleic Acid Simulations with Gromacs

Hi, On the gromacs webpage in user contributions-topologies you have (at least) 2 forcefields do download that allow you to simulate NA. The first is OPLS NA records from rnp-group (http://rnp-group.genebee.msu.su/3d/oplsa_ff.html). It is for gromacs 3.2.1, so minor manual adjustments for

Re: [gmx-users] Re: ANTECHAMBER GAFF

Dechang, With the help of Yang Ye and Mark, I downloaded amb2gmx.pl to transform the topology from AMBER format to GROMACS. But the script requires an AMBER installation to work and I didn't have a AMBER package. How can I go on? Mark pointed out one option -- rethink your choice of

Re: [gmx-users] Nucleic Acid Simulations with Gromacs

Please don't use the OPLS NA forcefield. It is largely based on AMBER (OPLS takes different approach in parameterization, so you know that direct migration is so correct) and not verified. I had some communications with that group on this issue. It has some teaching value on making topology of

Re: [gmx-users] Nucleic Acid Simulations with Gromacs

I would also suggest amber force field ports. I managed to run a simulation with Amber ff 99 and TIP3P water model in Gromacs. Good luck, Anna On 10/2/07, Monika Sharma [EMAIL PROTECTED] wrote: Dear All, I want to start nucleic acid simulations. I am using gromacs3.3.1. But I could not find

[gmx-users] Is there a test set for GROMACS 3.3.1 ?

Hi, The wiki refers to a test set for the upcoming 3.3.2 version. Is there a test set for the 3.3.1 version as well ? I tried running the test set for 3.3.2 after installing 3.3.1 and ran into a host of errors, but that is probably because of the different version ? Here are some of the errors

[gmx-users] mdrun error after 2.6nS

Hi all,The mdrun stopped after 2.6nS after writing this error:Step 1321571, time 2643.14 (ps) LINCS WARNINGrelative constraint deviation after LINCS:max 2.814066 (between atoms 2742 and 2745) rms 0.041434bonds that rotated more than 30 degrees:atom 1 atom 2 angle previous, current, constraint

Re: [gmx-users] mdrun error after 2.6nS

Hi Blaise, You'd better look in the log file where this starts. I bet it's either Lys-NH3+ or phosphate (ATP?) spinning like crazy. Check the archive for solutions. Best, Tsjerk On 10/2/07, Blaise Mathias-Costa [EMAIL PROTECTED] wrote: Hi all, The mdrun stopped after 2.6nS after writing

Re: [gmx-users] Is there a test set for GROMACS 3.3.1 ?

maria goranovic wrote: Hi, The wiki refers to a test set for the upcoming 3.3.2 version. Is there a test set for the 3.3.1 version as well ? I tried running the test set for 3.3.2 after installing 3.3.1 and ran into a host of errors, but that is probably because of the different version ?

Re: [gmx-users] Nucleic Acid Simulations with Gromacs

Thank you all for helping me. I will surely try the ffamber ports available. Regards, monika Yang Ye wrote: Please don't use the OPLS NA forcefield. It is largely based on AMBER (OPLS takes different approach in parameterization, so you know that direct migration is so correct) and not