[gmx-users] ATP for

2010-02-04 Thread Chandan Choudhury
Hello gmx users, I need to use ATP's parameter for amber port in gromacs. The atp.prep and frcmod.phos for ATP can be found at http://www.pharmacy.manchester.ac.uk/bryce/amber. How can I use it in ffamber. The program amb2gmx.pl needs amber to be installed, which is not present. Same with ACPYPI.

Re: [gmx-users] bonds section in the topology file

2010-02-04 Thread Justin A. Lemkul
Amir Marcovitz wrote: Thank you Justin, actually, i have two parallel rigid plates that are free to move towards each other on the Y-axis (i used position restrain on Y and Z axes) later on i will umbrella sampling to obtain the plate-plate PMF at various distances from each other (thanks a

Re: [gmx-users] bonds section in the topology file

2010-02-04 Thread Amir Marcovitz
Thank you Justin, actually, i have two parallel rigid plates that are free to move towards each other on the Y-axis (i used position restrain on Y and Z axes) later on i will umbrella sampling to obtain the plate-plate PMF at various distances from each other (thanks a lot for the helpful tutorial

Re: [gmx-users] grompp in GROMACS 4

2010-02-04 Thread Matthew L. Danielson
grompp in 4.0.7 doesn't use the -np flag anymore. You don't need it. In your example just do this: grompp_mpi -v -f _ _ _ mdrun_mpi -v -f -deffnm -np -Matt- edmund lee wrote: Dear all, I am new in Gromacs 4.0.7 before this I was using the GROMACS 3.3.3. I have some doubt in the grompp

Re: [gmx-users] grompp in GROMACS 4

2010-02-04 Thread Justin A. Lemkul
edmund lee wrote: Dear all, I am new in Gromacs 4.0.7 before this I was using the GROMACS 3.3.3. I have some doubt in the grompp commands when i want to run in parallel In Gromacs 3, I just use: grompp_mpi -v -f _ _ _ -np 4 then, mdrun_mpi -v -f -deffnm -np 4 but in Gromacs 4, I cant u

[gmx-users] grompp in GROMACS 4

2010-02-04 Thread edmund lee
Dear all, I am new in Gromacs 4.0.7 before this I was using the GROMACS 3.3.3. I have some doubt in the grompp commands when i want to run in parallel In Gromacs 3, I just use: grompp_mpi -v -f _ _ _ -np 4 then, mdrun_mpi -v -f -deffnm -np 4 but in Gromacs 4, I cant use 4 nodes in grompp

Re: [gmx-users] extending simulation confusion?

2010-02-04 Thread Justin A. Lemkul
nishap.pa...@utoronto.ca wrote: Hi, I am trying to extend my simulation time from 100ns -> 300ns. So I used the command : tpbconv -s old.tpr -extend 10 -o new.tpr but I got this: Extending remaining runtime of by 20 ps (now 14992 steps) Writing statusfile with starting step

Re: [gmx-users] a simple doubt about g_rms

2010-02-04 Thread Justin A. Lemkul
Miguel Quiliano Meza wrote: Hi everyone. Nowadays I am learning how to analyze my results after MD. I have been reading the tutorial "GROMACS Tutorial for Drug – Enzyme Complex" and all is fine but I have a big doubt about g_rms. I know that g_rms compares two structures by computing the ro

[gmx-users] extending simulation confusion?

2010-02-04 Thread nishap . patel
Hi, I am trying to extend my simulation time from 100ns -> 300ns. So I used the command : tpbconv -s old.tpr -extend 10 -o new.tpr but I got this: Extending remaining runtime of by 20 ps (now 14992 steps) Writing statusfile with starting step 0 and length 14992

[gmx-users] a simple doubt about g_rms

2010-02-04 Thread Miguel Quiliano Meza
Hi everyone. Nowadays I am learning how to analyze my results after MD. I have been reading the tutorial "GROMACS Tutorial for Drug – Enzyme Complex" and all is fine but I have a big doubt about g_rms. I know that g_rms compares two structures by computing the root mean square deviation (RMSD). In

Re: [gmx-users] bonds section in the topology file

2010-02-04 Thread Justin A. Lemkul
Amir Marcovitz wrote: Hi, i'm simulating a surface in water and ions which is composed of 6X6 Carbon atoms arranged on a 2-d lattice. (using ffamber99) i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom (or some other spacing of choice..), and to maintain the surfac

[gmx-users] bonds section in the topology file

2010-02-04 Thread Amir Marcovitz
Hi, i'm simulating a surface in water and ions which is composed of 6X6 Carbon atoms arranged on a 2-d lattice. (using ffamber99) i want to keep the spacing between C-C neighbouring atoms at 0.34 Angstrom (or some other spacing of choice..), and to maintain the surface rigid and planar for that i

gmx-users@gromacs.org

2010-02-04 Thread Ran Friedman
> fairuz zulkifli wrote: >> Hello everybody, >> I'm Fairuz from Malaysia. >> I just want to ask if there is someone that have information about >> PDB of ice and itp file of ice. >> I only had PDB of the ice and trying to convert it into itp file >> using GAMESS software. > > You can't. A .pdb fi

gmx-users@gromacs.org

2010-02-04 Thread Justin A. Lemkul
fairuz zulkifli wrote: Hello everybody, I'm Fairuz from Malaysia. I just want to ask if there is someone that have information about PDB of ice and itp file of ice. I only had PDB of the ice and trying to convert it into itp file using GAMESS software. You can't. A .pdb file is a coordinat

gmx-users@gromacs.org

2010-02-04 Thread fairuz zulkifli
Hello everybody, I'm Fairuz from Malaysia. I just want to ask if there is someone that have information about PDB of ice and itp file of ice. I only had PDB of the ice and trying to convert it into itp file using GAMESS software. Is there any suggestion? Thank you. -- gmx-users mailing listgmx

[gmx-users] CHARMM TIP3-Water with GMX

2010-02-04 Thread Stephane Abel
Hi all I am doing some tests with the CHARMM port in GROMACS. Before to start more extensive simulations with this ff I have performed a short run of 1000 TIP3-CHARMM water molecules in a cubic during at T=300 K and P=1.015 bar with v-rescale and PR as thermostat and barostat. I have used the

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

2010-02-04 Thread Mark Abraham
On 05/02/10 00:43, vivek sharma wrote: Hi Mark, Thanks for your response, it worked well for few molecule but not for all. As I mentioned first I am doing docking and then processing receptor through pdb2gmx and ligand through PRODRG server. But number of Hydrogen atoms in docked ligand and PRODR

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

2010-02-04 Thread vivek sharma
Hi Mark, Thanks for your response, it worked well for few molecule but not for all. As I mentioned first I am doing docking and then processing receptor through pdb2gmx and ligand through PRODRG server. But number of Hydrogen atoms in docked ligand and PRODRG generated topology are not same. Althou

Re: [gmx-users] Ligand coming out while trying Drug-enzyme tutorial

2010-02-04 Thread vivek sharma
Hi Tsjerk, Thanks for your response, I am finding problem in using original coordinates with the PRODRG topology because of mismatch in number of Hydrogen atoms in original coordinate file and PRODRG topology. Can you tell me how can I try 2nd option you suggested i.e. Fit the structure obtained fr

Re: [gmx-users] H2 topology

2010-02-04 Thread Mark Abraham
On 04/02/10 21:01, 011013021-Jyotsna wrote: Dear Mark, Your suggestions were very helpful . As per the literature I am following , It is required that the dummy atom has mass 0 and charge -0.950.Hence , I created the following itp file with this in mind. ## ; topology for hydrogen. [ molecul

[gmx-users] Re: tutorial for ionic liquid

2010-02-04 Thread Vitaly V. Chaban
Hi Catarina, This file contains the parameters for MD run, e.g. timestep, number of steps, etc. Good luck with IL, Vitaly -- Vitaly V. Chaban, Ph.D. http://www-rmn.univer.kharkov.ua/chaban.html On Thu, Feb 4, 2010 at 2:39 PM, Catarina Nunes wrote: > Sorry Vitaly, > Can you tell me what mean

Re: [gmx-users] H2 topology

2010-02-04 Thread 011013021-Jyotsna
Dear Mark, Your suggestions were very helpful . As per the literature I am following , It is required that the dummy atom has mass 0 and charge -0.950.Hence , I created the following itp file with this in mind. ## ; topology for hydrogen. [ moleculetype ] ;namenrexcl H2 2 [ at