Re: [gmx-users] PRODRG tools

Actually, you can use other parametrization tools like antechamber (for amber) or cgenff (for charmm). Liu Shiyong wrote: Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. You can

Re: [gmx-users] PRODRG

I think that is better to use antechamber tools. On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me

Re: [gmx-users] PRODRG

I'm completely in agreement with that advice. To use antechamber tool, I recommend use force field for all the system. The OP's question is easily answered by referring to the PRODRG FAQ in dealing with proper protonation. As for Antechamber and the like, these are good tools, but do not

[gmx-users] multiplicity for qmmm simulations

Dear gmx-users I have tried to perfomed some simulations about protein dynamics, including one copper ion around the protein by Gromacs/CPMD. However, when I put the multiplicity value in the input file is ok, but in the CPMD_inp.run file doesn't appear. These are my files: em.mdp: I printed

[gmx-users] Binding energy for two proteins

Dear all. A few days ago I posted a question related with binding energy between two proteins using the LIE method, in that case my energies were between -2400 to -2700 kcal/mol. Later, I tried to obtain the same information doing several simulations employing the FEP method in combination with

[gmx-users] LIE energy values for dimers

Dear all I used LIE method in order to obtain information related with free energy bind between two proteins. Previously, I obtained several dimeric configuration using zdock package, and geometry optimization for each model. For the first ten complex, I used LIE. These are my results:

Re: [gmx-users] LIE energy values for dimers

Thanks a lot professor Spoel! On 2010-03-13 20.13, jorge_quint...@ciencias.uis.edu.co wrote: Dear all I used LIE method in order to obtain information related with free energy bind between two proteins. Previously, I obtained several dimeric configuration using zdock package, and

[gmx-users] Free Energy Calculations

Hello all. I worked with free energy calculations to obtain some information related with solvation and binding free energy, analizing two proteins and using amber94 force field. But, I have two questions. 1. When I tried to do a minization energy, I got the following message: WARNING 1

[gmx-users] Free Energy Calculations

Hello everybody I tried to work with gromacs employing free energy calculations in a dimeric protein system. First of all, doing a energy minimization a later to compute the binding energy. For all the cases, I use amber 94 FF. However, I have two questions. 1. When I made the energy

Re: [gmx-users] Problems with gromacs-openMM

Thanks a lot!!! it works Hi, try to do add the OpenMM library dir to your library path before running make $ export LD_LIBRARY_PATH=/opt/openmm/lib:$LD_LIBRARY_PATH Also, OpenMM support will be officially available in the next Gromacs release (soon). Rossen On 1/27/10 4:28 AM,

[gmx-users] Problems with gromacs-openMM

Hello everybody, I tried to install gromacs 4.0.7 + openMM on Fedora core 10 x86_64, but I had lots of problems with that. I typed the configure options below to obtain a Makefile: $ ./configure --enable-shared --prefix=/opt/gromacs_openmm CPPFLAGS=-I/opt/openmm/include/openmm/

[gmx-users] Problem with Gromacs-CPMD

Dear all, I'm running some simulations using Gromacs/CPMD but it doesn't continue during QMCONTINUE file lecture. See below: EXTERNAL ENERGY= 5.867019924829098E-002 AU REAL TOTAL ENERGY = -97.3517503273190 AU ATOM COORDINATESGRADIENTS (-FORCES) 1 C

[gmx-users] Solvation Free energy using Amber

Dear all. I've tried to calculate solvatin free energy using amber force field and gromacs but unfourtunately I can't include the parameters for B type. Can somebody help me with that, I send you a top file. Best regards, Jorge R. Quintero Grupo de Investigación en Fisicoquímica Teórica y

Re: [gmx-users] Solvation Free energy using Amber

Dear Justin I removed the semicolons but my calculations don't work. The problem is how can I add the other parameters -like bonds, angles and dihedrals- for B-state. I've tried to add it, but I get some problems to obtain the tpr file. Thanks again. [ bonds ] 1 2 1 -- how can I

Re: [gmx-users] Solvation Free energy using Amber

Well, The main reason why I've testedd to obtain solvation free energy (SFE) for toluene is because I want to do it for my future studies related with dimer SFE employing Amber force field with gromacs 4.0. Recently, I've read the tutorial. But, when I tried to do the same, I got some errors

Re: [gmx-users] Solvation Free energy using Amber

Ok, thank you for your time. jorge_quint...@ciencias.uis.edu.co wrote: Ok Justin, I send You a copy of muy simulation for SFE with two proteins + water. Look the top file structure. Thanks again. A quick look at the topologies indicates to me that something is badly broken. The net

[gmx-users] Free energy calculations

I'm interesting to calculate Gibbs energy using g_lie application. Unfourtunately, I don't know what kind of state equation is the sub-program using. Can you help me with that. Best regards Jorge R. Quintero Grupo de Investigación en Fisicoquímica Teórica y Experimental Universidad Industrial

Re: [gmx-users] PRODRG

Hello Chanel Could you send a copy of the PDB file. I think that the error is related with label atoms included in each force fiel parameter. See you. Hello, I have recently made a pdb file using the Dundee PRODRG server. However, when I try to use this pdb in gromacs, I receive an

[gmx-users] Problems with metals GROMACS/CPMD

Hello all. I have tried to perfomed some simulations about protein dynamics, including one copper ion around the protein by Gromacs/CPMD. However, I get some problems during CPMD simulation. In the *.mdp file I added the following:

[gmx-users] Problems with GROMAC/CPMD

Hello all. I have tried to perfomed some simulations about protein dynamics including one copper ion, close from the protein, by Gromacs/CPMD. However, I get some problems during CPMD simulation. In the *.mdp file I added the following: