[gmx-users] No such moleculetype Na

Hi, I am performing the simulation of DNA in Gromacs using AMBER03 force field. The charge on the system is large (-23). I get grompp error when I add the relevant number of Na+ atoms. Program grompp_mpi, VERSION 3.3.1 Source code file: toppush.c, line: 1293 Fatal error: No such moleculetype Na

Re: [gmx-users] No such moleculetype Na

Hi Swati, > Fatal error: > No such moleculetype Na > > But the atom type is present in ffamber03.rtp. I tried changing the atom > name to NA and Na+. But I still get similar error. Kindly help. It doesn't complain about the atom type, but about the moleculetype. Did you #include "ions.itp"? That

Re: [gmx-users] No such moleculetype Na

Hi Tsjerk, Thanks for your reply. ions.itp is already included in topology file. However after you mentioned I checked the ions.itp file. But I think it defines molecule type only for gromacs force fields and the OPLS force field. The headers are only these three #ifdef _FF_GROMACS #ifdef _FF_GROMO

[gmx-users] -center -fit dodecahedron : dimer

Dear Gromacs Users,   I am performing a MD simulation of a dimer in a dodecahedron box. The simulation stopped after 8 ns (power cut) and i had to restart to complete it fully to 12 ns.   I then concatenated the two trajectories using trjcat   trjconv -f promd.trr -s proem.tpr -pbc nojump -o noj

Re: [gmx-users] No such moleculetype Na

Hi Swati, Sorry, I wasn't paying that much attention indeed and failed to notice you were dealing with Amber. There's nothing wrong with your installation in this regard; Gromacs just does not have Amber included by default. I'm not sure if there's an ions.itp for Amber somewhere, but it's not to

Re: [gmx-users] -center -fit dodecahedron : dimer

Hi Nahren, > trjconv -f promd.trr -s proem.tpr -pbc nojump -o nojump.xtc > trjconv -f nojump.xtc -s proem.tpr -pbc mol -ur compact -center -boxcenter > tric -o center.xtc > trjconv -f center.xtc -s proem.tpr -fit rot+trans -o fit.xtc > 1. The above procedures does not center the molecule in the

Re: [gmx-users] -center -fit dodecahedron : dimer

nahren manuel wrote: Dear Gromacs Users, I am performing a MD simulation of a dimer in a dodecahedron box. The simulation stopped after 8 ns (power cut) and i had to restart to complete it fully to 12 ns. I then concatenated the two trajectories using trjcat trjconv -f promd.trr

[gmx-users] g_cluster output

Hi, I have a query regarding "g_cluster" output. I gave the command g_cluster -f ../const_temp_20ns_0.pdb -s ../../md_0.tpr -sz -tr -cl -wcl 25 -cutoff 0.2 It is written in the "clusters.log" file that the middle structures of each cluster is written in the "clusters.pdb" file. How is t

Re: [gmx-users] -center -fit dodecahedron : dimer

Dear Gormacs User, I have now created a new tpr in which the protein is centered. trjconv -f promd.xtc -s tprdodecasolv.tpr -center -boxcenter tric -pbc mol -ur compact -o center.xtc trjconv  -s tprdodecasolv.tpr -fit rot+trans -f center.xtc -o fit.xtc I see the dimer getting split in some of th

Re: [gmx-users] g_cluster output

sarbani chattopadhyay wrote: Hi, I have a query regarding "g_cluster" output. I gave the command g_cluster -f ../const_temp_20ns_0.pdb -s ../../md_0.tpr -sz -tr -cl -wcl 25 -cutoff 0.2 It is written in the "clusters.log" file that the middle structures of each cluster is written in the "clus

Re: [gmx-users] -center -fit dodecahedron : dimer

nahren manuel wrote: Dear Gormacs User, I have now created a new tpr in which the protein is centered. trjconv -f promd.xtc -s tprdodecasolv.tpr -center -boxcenter tric -pbc mol -ur compact -o center.xtc trjconv -s tprdodecasolv.tpr -fit rot+trans -f center.xtc -o fit.xtc I see the dimer get

[gmx-users] Re:binding energy

Hi, I am performing MD simulations for peptide(ligand)-receptor complex. I dont know how to calculate the binding energy for the complex and individual structures using gromacs version 4. Can anyone please help me out. Regards, Archana. ___ gmx-us

Re: [gmx-users] No such moleculetype Na

Hi Tsjerk, Thanks for your suggestion.I tried to change the ions.itp as follows : #ifdef _FF_AMBER03 [ moleculetype ] ; molname nrexcl Na+ 1 [ atoms ] ; idat type res nr residu name at name cg nr charge 1 Na 1 Na Na 1 1 #end

[gmx-users] Identical energies generated in a rerun calculation ... but ...

Dear users, I am experiencing some troubles in using GMX 4.0.4 trying to rerun trajectories and obtaining energies for single residues and/or portion of proteins. According to the mdrun command help and to my experience with the previous versions of GROMACS, I have edited my mdp file including

Re: [gmx-users] Identical energies generated in a rerun calculation ... but ...

Luca Mollica wrote: Dear users, I am experiencing some troubles in using GMX 4.0.4 trying to rerun trajectories and obtaining energies for single residues and/or portion of proteins. According to the mdrun command help and to my experience with the previous versions of GROMACS, I have edited

Re: [gmx-users] No such moleculetype Na

Hi Tsjerk, Thanks for your suggestions.After including molecule types from ions.itp for OPLS force field,its working fine now. Thanks again. Regards, Swati > Hi Swati, > > Sorry, I wasn't paying that much attention indeed and failed to > notice you were dealing with Amber. There's nothing wron

[gmx-users] RMSD of Aminoacids

Hi, I'm trying to compare two proteins with the same number of aminoacids with g_confrms, and it works all right, but it gives me the RMSD of the hole protein, and I need the distances (or deviations) of each aminoacid. I know this data shoul be there, but I don't know how to get it (I've got the m

RE: [gmx-users] about the bond connection between different groups

Hi Tsjerk, Thank you for your reply. SO you mean I can just define the bond in one moleculetype.As what you said, I have to renumber all atoms from one of the moleculetypes, starting at N+1, with N being the number of the last atom of the first moleculetype .Then I wonder which molecule type t

Re: [gmx-users] about the bond connection between different groups

You have: [ moleculetype ] A [atoms] 1 ... N and [ moleculetype ] B [atoms] 1 ... M and want to make a bond between atom X of A and Y of B. So you have to merge A and B into: [ moleculetype ] A+B [atoms] 1 ... N N+1 ... N+M with a.o.: [bonds] X Y+N type bond-parameters. I hope this is clear

RE: [gmx-users] about the bond connection between different groups

Hi Tsjerk, Thank you very much for your introduction about how to merge two moleculetypes. I just follow your instructions as listed below; I have two moleculetypes named DNA and ICE. This is what I include in topology file: #include "dna.itp" #include "ICE.itp" [ moleculetype ] ; molname

[gmx-users] np command with GROMACS 4.0.4

Hi! I am trying to do my position restrained dynamic simulation on GROMACS 4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus; I typed in the following grompp command: grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx -maxwarn 10 and it gave me the

Re: [gmx-users] np command with GROMACS 4.0.4

Halie Shah wrote: Hi! I am trying to do my position restrained dynamic simulation on GROMACS 4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus; I typed in the following grompp command: grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx -maxwa

Re: [gmx-users] np command with GROMACS 4.0.4

Halie Shah wrote: Hi! I am trying to do my position restrained dynamic simulation on GROMACS 4.0.4, and I want to use 4 nodes on the cpu cluster available at my campus; I typed in the following grompp command: grompp -np 4 -f pr.mdp -c BR6_em.pdb -p BR6.top -o BR6_pr.tpr -n prot.ndx -max

RE: [gmx-users] np command with GROMACS 4.0.4

You don't need to use -np 4 option to do preprocessing on version 4.0.4. Just do preprocessing without it and use it when you start your simulation like followings: grompp mpirun -np 4 mdrun (if you use MPI for parallel running) kyungchan From: gmx-users-boun...@gromacs.org [mailto:gm

Re: [gmx-users] about the bond connection between different groups

Dear Yang, It appears that you will either need to either A) create a new index file using the make_ndx utility, or B) modify your existing index file. If you haven't done this procedure before, the first option may be the easiest. A good description of make_ndx is contained in the manual as

Re: [gmx-users] about the bond connection between different groups

He, Yang wrote: Hi Tsjerk, Thank you very much for your introduction about how to merge two moleculetypes. I just follow your instructions as listed below; I have two moleculetypes named DNA and ICE. This is what I include in topology file: #include "dna.itp" #include "ICE.itp" Depending

[gmx-users] Re: np command with GROMACS 4.0.4

If seems in the gmx versions above 4.0 '-np' is not used. If I am not mistaken you should just point out the number of nodes in your queueing system while submitting the job. Vitaly > I am trying to do my position restrained dynamic simulation on GROMACS > 4.0.4, and I want to use 4 nodes on th

Re: [gmx-users] RMSD of Aminoacids

Andy Torres wrote: Hi, I'm trying to compare two proteins with the same number of aminoacids with g_confrms, and it works all right, but it gives me the RMSD of the hole protein, and I need the distances (or deviations) of each aminoacid. I know this data shoul be there, but I don't know how to

[gmx-users] problem in topology file of protein-lipid bilayer system for grompp

Dear Justin I am doing simulation of membrane protein .I follow your tutorial for that I think its perfect for that. But I am getting problem in doing inflategro step, I alredy discuss this problem with you but now I am starting everything fresh I have completed upto c

[gmx-users] validating gromacs installation 4.0.4

Dear Users, I posted the following message a few days ago; So far I have not got any response. Searching archives also seem to indicate that people are facing similar problems. Some times modifying mdp options make the tests "pass" as we also observed ( see below ). Further the reference traje

Re: [gmx-users] problem in topology file of protein-lipid bilayer system for grompp

nitu sharma wrote: Dear Justin I am doing simulation of membrane protein .I follow your tutorial for that I think its perfect for that. But I am getting problem in doing inflategro step, I alredy discuss this problem with you but now I am starting everything fresh