Re: [gmx-users] Charge on drug

Thank you I have generated the itp file from ATB. It works fine. On Wed, Dec 21, 2016 at 7:48 AM, Justin Lemkul wrote: > > > On 12/19/16 1:23 PM, tasneem kausar wrote: > >> Thank you for reply >> What type of refinements are needed in topolgy file. >> I have created the topology file from pdb f

Re: [gmx-users] Charge on drug

On 12/19/16 1:23 PM, tasneem kausar wrote: Thank you for reply What type of refinements are needed in topolgy file. I have created the topology file from pdb file. Mol2 was converted into pdb and sdf of pubchem was converted into mol2. So sdf to mol2 to pdb. And please suggest me the right choi

Re: [gmx-users] Charge on drug

Thank you for reply What type of refinements are needed in topolgy file. I have created the topology file from pdb file. Mol2 was converted into pdb and sdf of pubchem was converted into mol2. So sdf to mol2 to pdb. And please suggest me the right choice of server for itp file generation. Thanks i

Re: [gmx-users] Charge on drug

On 12/19/16 5:31 AM, tasneem kausar wrote: Thanks for reply I have visualized solvate.gro and em.gro. Some bonds that are not present in box.gro is seen in em.gro. I am giving you the link of the file to visualize. https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE https://drive.goo

Re: [gmx-users] Charge on drug

solvate.gro is box.gro file. It was typing mistake. On Mon, Dec 19, 2016 at 4:01 PM, tasneem kausar wrote: > Thanks for reply > > I have visualized solvate.gro and em.gro. Some bonds that are not present > in box.gro is seen in em.gro. > I am giving you the link of the file to visualize. > https

Re: [gmx-users] Charge on drug

Thanks for reply I have visualized solvate.gro and em.gro. Some bonds that are not present in box.gro is seen in em.gro. I am giving you the link of the file to visualize. https://drive.google.com/open?id=0B51QL37xf6MKNXlVT2VHSEM5YVE https://drive.google.com/open?id=0B51QL37xf6MKMTByZmR1MURGTXM I

Re: [gmx-users] Charge on drug

Hi, Your energy minimization literally cannot create bonds because those are already defined by your topology. See http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds for what's probably going on. Mark On Mon, 19 Dec 2016 19:05 tasneem kausar

[gmx-users] Charge on drug

Dear All I am using Acpype server to generate topology file of drug molecule to perform protein drug MD simulation. Acpype have generated the itp file and other necessary for MD simulations. I am doing MD on gromacs 5.1.4 software using amber99sb force field. When I have done energy minimization