Re: [gmx-users] Protein preparation

On 3/30/17 9:59 AM, Quin K wrote: Thank you. There are so many pdb structures for the protein I'm looking for. I'm not sure which one to pick. What should I look for when picking a protein pdb structure? I want to test for an inhibitor with the protein. Which of the following I should look

Re: [gmx-users] Protein preparation

Thank you. There are so many pdb structures for the protein I'm looking for. I'm not sure which one to pick. What should I look for when picking a protein pdb structure? I want to test for an inhibitor with the protein. Which of the following I should look for. Resolution Ligands Inhibitors

Re: [gmx-users] Protein preparation

On 3/27/17 2:16 AM, Rasika Kelum wrote: Thank you Justin. Highly appreciate your help. If there are missing residues, any suggestions on fixing the protein? There are plenty of tools to do that; Modeller is one of them. 1. How to find correct sequence? (is there any website to find

Re: [gmx-users] Protein preparation

Thank you Justin. Highly appreciate your help. If there are missing residues, any suggestions on fixing the protein? 1. How to find correct sequence? (is there any website to find correct sequence?) 2. How to FIX the sequence (using what software?) 3. Once residues are fixed how would that

Re: [gmx-users] Protein preparation

On 3/26/17 12:39 PM, Quin K wrote: Thank you for the reply. I have another question. I used MODELLER on Chimera to fix the protein and found that there were significant visible changes to structure of protein. I'm not sure whether to use the old protein or the fixed one. Does it really matter

Re: [gmx-users] Protein preparation

Thank you for the reply. I have another question. I used MODELLER on Chimera to fix the protein and found that there were significant visible changes to structure of protein. I'm not sure whether to use the old protein or the fixed one. Does it really matter that I used unfixed protein if the

Re: [gmx-users] Protein preparation

On 3/26/17 9:44 AM, Quin K wrote: Hi I'm new to Gromacs. I have a question regarding protein preparation for MD simulation. I ran a 50 ns MD simulation but later found out that the protein has a charge. I found that there is a Mg2+ Ion in the protein crystal structure. Should I remove this

[gmx-users] Protein preparation

Hi I'm new to Gromacs. I have a question regarding protein preparation for MD simulation. I ran a 50 ns MD simulation but later found out that the protein has a charge. I found that there is a Mg2+ Ion in the protein crystal structure. Should I remove this Mg2+ ion from protein before addition

[gmx-users] Protein preparation in Membrane simulation

Dear all When doing membrane simulation, do protein needs to be prepared in Xleap module in Amber as given in tutorials (Bevans Lab). regards -- B.Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before