[gmx-users] How to solve GBSA problem ?

Dear Experts, Hi, I am using OPLSAA forcefiled and tried to use implicit solvent. But There may be some problems. how can i solve this problem?? GB parameter(s) missing or negative for atom type 'opls_267' GB parameter(s) missing or negative for atom type 'opls_269' GB parameter(s) missing or neg

[gmx-users] Residue 'HEM' not found in residue topology database

Dear all,   I am having the troubles to obtain the topology file for Cytochrome C.  When I used the Gromos96 53a6 force filed in the GROMACS 4.0.7 software package, the topology file is produced, but there is lack of some force field parameters, such as  the bonds from Cys 14 and Cys 17 to the p

Re: [gmx-users] Residue 'HEM' not found in residue topology database

On 14/04/2011 5:59 PM, hui sun wrote: Dear all, I am having the troubles to obtain the topology file for Cytochrome C. When I used the Gromos96 53a6 force filed in the GROMACS 4.0.7 software package, the topology file is produced, but there is lack of some force field parameters, such as the

Re: [gmx-users] How to solve GBSA problem ?

On 14/04/2011 5:34 PM, Hyunsik wrote: Dear Experts, Hi, I am using OPLSAA forcefiled and tried to use implicit solvent. But There may be some problems. how can i solve this problem?? GB parameter(s) missing or negative for atom type 'opls_267' GB parameter(s) missing or negative for atom type '

[gmx-users] Re: EDO and TRS ligand

Ahmet, Please refrain from sending personal e-mails, unless you're invited to do so. > I am working on the EDO and TRS ligands for 2/3 weeks.But I dont solved it. > Please help me. This is what supervisors are for. I assume you have one. > I am using the wavefunction spartan 8 program to calcul

Re: [gmx-users] Re: EDO and TRS ligand

On 14/04/2011 7:06 PM, Tsjerk Wassenaar wrote: I am using the wavefunction spartan 8 program to calculate charges. revised_EDO.itp ... [ moleculetype ] ; Name nrexcl EDO 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1OA 1 EDO OAB 1 -0

[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3

Dear Gromacs users, I got different free energy values by Thermodynamic Integration (TI) in Gromacs 4.0.7 and 4.5.3. When I calculated the hydration free energy of Chloride ion by using Thermodynamic Integration method, the results for the free energy of un-charging the Chloride ion from q=-e

[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3

Dear Gromacs users, I got different free energy values by Thermodynamic Integration (TI) in Gromacs 4.0.7 and 4.5.3. When I calculated the hydration free energy of Chloride ion by using Thermodynamic Integration method, the results for the free energy of un-charging the Chloride ion from q=-e

[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3

Dear Gromacs users, I got different free energy values by Thermodynamic Integration (TI) in Gromacs 4.0.7 and 4.5.3. When I calculated the hydration free energy of Chloride ion by using Thermodynamic Integration method, the results for the free energy of un-charging the Chloride ion from q=-e

[gmx-users] binding_affinity

Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahid Nayeem -- gmx-users ma

Re: [gmx-users] binding_affinity

shahid nayeem wrote: Dear All I have some protein complex pdb after docking two monomers. The scoring of these docked structure are not true representative of binding affinity. I want calculate the binding affinity affinity of these docked pdb. Can anyone suggest me, how should I proceed. Shahi

[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

Dear users, pdb2gmx -f xxx.pdb water:spc forcefield:43a1 editconf -f conf.gro -bt cubic -d 1.0 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal error:* number of coordinates in coordinate file (solvated.gro, 10

[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3

Dear Yan: If you want to get to the bottom of this then (a) please report your mdp files and (b) show some evidence that your values are converged by, for instance, block averaging the run-time. Chris. -- original message -- Dear Gromacs users, I got different free energy values by The

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

ahmet yıldırım wrote: Dear users, pdb2gmx -f xxx.pdb water:spc forcefield:43a1 editconf -f conf.gro -bt cubic -d 1.0 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr *Fatal error:* number of coordinates in coordin

[gmx-users] tip5p.gro

Dear Justin, I found out that as you had said, my naming wasn't consistent. I checked and manipulated all file in share/top. i didn't have any problem with files flexwaterguson.itp, atommass.dat, spc.itp, spce.itp, spc216.gro and tip3.itp but when it comes to files tip4p.gro and tip5p.gro I hang.

Re: [gmx-users] tip5p.gro

On 15/04/2011 12:04 AM, sarah k wrote: Dear Justin, I found out that as you had said, my naming wasn't consistent. I checked and manipulated all file in share/top. i didn't have any problem with files flexwaterguson.itp, atommass.dat, spc.itp, spce.itp, spc216.gro and tip3.itp but when it come

[gmx-users] Installation error

I have already posted this error report on 6 Dec 2010 but still have not getting any solution. So I am thankful if any one can rectify the solution of installation problem i.e. While installing gromacs-4.5.3 I got an error on executing make command. I am installing this gromacs version on cygwin. T

[gmx-users] micelles and trjconv -pbc cluster

Dear GROMACS users,    I am trying to simulate an SDS micelle in water. As simulation time goes by, the micelle approaches the edge of the box and consequently some of these molecules get in from the other side. This leads to incorrect radius of gyration, eccentricity, etc. A solution to this

Re: [gmx-users] micelles and trjconv -pbc cluster

jim jack skrev 2011-04-14 16.42: Dear GROMACS users, I am trying to simulate an SDS micelle in water. As simulation time goes by, the micelle approaches the edge of the box and consequently some of these molecules get in from the other side. This leads to incorrect radius of gyration, ecce

Re: [gmx-users] Different TI free energy values in 4.0.7 and 4.5.3

Dear Gromacs users, One example of my mdp files with lambda=0.5 is like the following: integrator = md tinit= 0 dt = 0.004 nsteps = 25 simulation_part = 1 comm_mode= Linear nstcomm

Re: [gmx-users] micelles and trjconv -pbc cluster

Hi George, Recently I wrote an alternative, non-iterative clustering routine, that does not suffer from convergence failures. If you want, I can send you the modified trjconv source code. Note that it does not bother about the center of mass of the cluster, but just builds a network of neighbours,

Re: [gmx-users] OPLS with Water models

Hi Justin, Thanks for the reply and the reference. I knew that I am asking for a broad question. OPLS will work for my protein problem. The reason why I am asking the question is to know how diffirent water models work for OPLS and is there any comparison work done for it. The reference you mentio

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

Dear Justin, I built .rtp entries for two ligands using ( http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top the following parts: #include "TRS.itp" #include "EDO.itp" TRS 1 EDO 6 Furthermore I added the number of atoms (20) in the second line of t

Re: [gmx-users] micelles and trjconv -pbc cluster

On 15/04/2011 12:42 AM, jim jack wrote: Dear GROMACS users, I am trying to simulate an SDS micelle in water. As simulation time goes by, the micelle approaches the edge of the box and consequently some of these molecules get in from the other side. This leads to incorrect radius of gyratio

Re: [gmx-users] Installation error

On 15/04/2011 12:29 AM, pawan raghav wrote: I have already posted this error report on 6 Dec 2010 but still have not getting any solution. So I am thankful if any one can rectify the solution of installation problem i.e. While installing gromacs-4.5.3 I got an error on executing make command. I

[gmx-users] RE: micelles and trjconv -pbc cluster

gy * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110414/2adc27d7/attachment.html -- -- gmx-use

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

ahmet yıldırım wrote: Dear Justin, I built .rtp entries for two ligands using (http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top the following parts: #include "TRS.itp" #include "EDO.itp" Well, either pdb2gmx built the molecules into your topology or you're #including

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

Dear Justin, Thanks for your valuable helps. How should I rearranged the conf.gro file for 6 EDO ligand? is the following conf.gro mistake? *conf.gro:* MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE 5354 2GLN N1 1.458 -1.158 0.739 2GLN H12 1.520 -1.083 0.763 ... 485HO

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

ahmet yıldırım wrote: Dear Justin, Thanks for your valuable helps. How should I rearranged the conf.gro file for 6 EDO ligand? is the following conf.gro mistake? Well, it's certainly not working, is it? You only have one EDO molecule shown here. Is this the only one? If it is, then y

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

On 14 April 2011 02:11, Mark Abraham wrote: > On 14/04/2011 3:40 PM, Moeed wrote: > > > > On 13 April 2011 18:45, Mark Abraham wrote: > >> On 14/04/2011 10:22 AM, Moeed wrote: >> >> Hello, >> >> I have run 2 ns simulations on a hydrocarbon system (initial density of ~ >> 2 SI and box size is 1

[gmx-users] Adding Virtual Site to the Molecule

Hi I am thinking of a simulation set up, where I modify a structure/topology of a molecule under consideration, in which, I want to introduce a dummy atom/site which will always be located at center of mass of a molecule and it will only interact with dummy atom of other molecule. I am not sure h

[gmx-users] Re: micelles and trjconv -pbc cluster

Dear Ran Friedman and Tsjerk Wassennaar,    First of all, thanks to all responses to my problem. As far as the modified versions of g_clustsize and trjconv, I really want to try them.  Best regards  George Koros --- On Thu, 4/14/11, jim jack wrote: From: jim jack Subject: micelles and trjconv

[gmx-users] genbox

I have .gro and .top of a nanoparticle at temperature 1K and I want to add the simulation box some other atomes at temperature 300K. is there any body knows how can I do it. I have used (genbox -cp nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it add more than atomes than I ex

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

Moeed wrote: On 14 April 2011 02:11, Mark Abraham > wrote: On 14/04/2011 3:40 PM, Moeed wrote: On 13 April 2011 18:45, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote: On 14/04/2011 10:22 AM, Moeed wrote: Hello, I hav

Re: [gmx-users] genbox

leila separdar wrote: I have .gro and .top of a nanoparticle at temperature 1K and I want to add the simulation box some other atomes at temperature 300K. is there any body knows how can I do it. I have used (genbox -cp nanoparticle.gro -ci otheratom.gro -p nanoparticle.top -o out) but it add

Re: [gmx-users] Re: micelles and trjconv -pbc cluster

Dear Tsjerk and Ran, I would like to try your modified versions of g_clustsize and trjconv as well since I am facing similar issues on the analyses of micellar systems. with kind regards, Andre On Thu, Apr 14, 2011 at 5:29 PM, jim jack wrote: > Dear Ran Friedman and Tsjerk Wassennaar, > > >

[gmx-users] integral equation theory in gromacs?

Hi, I was wondering whether there is any way in gromacs so that one can perform integral equation theory or RISM theory of a system . Sanku-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

On 15/04/2011 5:55 AM, Moeed wrote: On 14 April 2011 02:11, Mark Abraham > wrote: On 14/04/2011 3:40 PM, Moeed wrote: On 13 April 2011 18:45, Mark Abraham mailto:mark.abra...@anu.edu.au>> wrote: On 14/04/2011 10:22 AM, Moeed wrote:

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

So Sorry I did not mean to be rough :) . Thanks for your comments...:) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subs

Re: [gmx-users] NPT issue in 4.0.7 and 4.5.3

On 15/04/2011 10:29 AM, Moeed wrote: So Sorry I did not mean to be rough :) . Thanks for your comments...:) No no, no problem. By "rough", I meant being rough on the simulation system, with conditions too strenuous :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gro

Re: [gmx-users] integral equation theory in gromacs?

I know that 3-D RISM with the Kovalenko-Hirata closure for solvent has been applied to and is available in the most recent AMBER package. [J. Chem. Theory Comput., 2010, 6 (3), pp 607–624] Pande did a study of MD applications of 3-D RISM this year [J. Phys. Chem. B, 2011, 115 (2), pp 319–328] sp

Re: [gmx-users] micelles and trjconv -pbc cluster

Hey :) As there seems to be interest :) Below is the diff between native and my version of gmx_trjconv.c 4.5, the complete source file is attached. I'd fancy comments and suggestions. Hope it helps, Tsjerk ### 82a83,208 > static void taw_pbc_cluster(int nrefat,t_topology *top,rvec *x, atom_id

Re: [gmx-users] Installation error

You are really PATIENT waiting for FOUR months for the answers. Ask the person around you they might be able to provide useful suggestions. There might be some libs linking problem. I have never tried the Cygwin, you may really try "searching" first before "waiting". lina P.S if I were you, I

[gmx-users] Re: Trajectory visualization

Hi, I have done a simulation of 10ns but while viewing the trajectory in VMD I am getting some problems. After loading the .gro and .xtc file VMD stops working .. I used trjconv to compress the file but VMD doesnot read frames from tat file... How can I visualize the trajectories?? -- Bharat Ph.

Re: [gmx-users] Re: Trajectory visualization

On 15/04/2011 2:49 PM, bharat gupta wrote: Hi, I have done a simulation of 10ns but while viewing the trajectory in VMD I am getting some problems. After loading the .gro and .xtc file VMD stops working .. I used trjconv to compress the file but VMD doesnot read frames from tat file... How ca

Re: [gmx-users] Re: Trajectory visualization

Reduicng no. of frames means breaking the simulation into smaller frames ... will it affect the result ?? On Thu, Apr 14, 2011 at 10:06 PM, Mark Abraham wrote: > On 15/04/2011 2:49 PM, bharat gupta wrote: > >> Hi, >> >> I have done a simulation of 10ns but while viewing the trajectory in VMD I >>

Re: [gmx-users] Re: Trajectory visualization

On 15/04/2011 3:08 PM, bharat gupta wrote: Reduicng no. of frames means breaking the simulation into smaller frames ... will it affect the result ?? You can use trjconv -dt to reduce the number of frames per unit time, not just chopping into segments. Whether it affects your result is somethi

[gmx-users] RE: micelles and trjconv -pbc cluste

Hi, I've sent the program off list. I hope to have a version compatible with the current or future version of Gromacs and will then upload it to the user contributions. Ran -- Message: 2 Date: Thu, 14 Apr 2011 13:29:42 -0700 (PDT) From: jim jack Subject: [gmx-users]