[gmx-users] PRODRG

[Soren Wacker]

Hi, 

I think, you should avoid the PRODRG server. If you use it, take care with the validation of you parameters. Especially, the charges. There are different tools which can generate topologies and pdb files. To could use RDkit to generate coordinates save it as SDF convert it to  PDB with e.g. OpenBabel. Other useful tools would you may consider are MarvinSketch and Antechamber (Ambertools). Which conformer to use depends on which conformer/s you are interested in. 

best
Soren

--
Dr. Soeren Wacker
Centre For Molecular Simulation, BI # 547
The University of Calgary
2500 University Drive (NW)
Calgary, Alberta
Canada, T2N 1N4

Tel.:   ++1 (403) 210 7860
Email:  swacker at ucalgary.ca

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Negar Parvizi [negar.parvizi at yahoo.com]
Sent: Monday, May 26, 2014 11:00 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] PRODRG

Dear all users,

I am using Protein-Ligand Complex tutorial (Justin Lemkul tutorial). For making .pdb file of ligand, we should use PRODRG(draw molecule with JME Editor).
 Here is my question that when i draw my ligand in JME Editor, which conformer should i select ? because different conformer gives different PRODRG output files.

Thanks in advance,
N.Parvizi
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