[gmx-users] problem while running grompp command

Hi all. I am doing dynamics studies of protein-ligand dynamics.When I am running grompp command error is coming "atomtype SDMSO NOT FOUND" . I checked in drg.itp file [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 OM 1 LIG OXT 1 -0.758 15.9994 2 C 1 LIG C 1 0.362 12.0110 3 OM 1 LIG O 1 -0.

[gmx-users] problem regarding npt equilibration

HI all.. I am doing npt of protein-ligand complex. Now in that error is coming"Pressure scaling more than 1%". How can I overcome this problem? -- [image: images[12]] “Many Smiles Begin Because Of Another Smile . . . ." Regards, Rashi <>-- gmx-users mailing listgmx-users@gromacs.org http:

[gmx-users] need help

Hi all I have an ligand having NI atom(Nickel) .Now problem is this when I am running PRODRG server ,ligand topology can not be created and error is coming *unsupported atom type NI (atom 'NI2 ') in your coordinates*.now how to overcome this problem? plz help me!! -- [image: images[12]] “Many

[gmx-users] problem using trjconv command

Hi all . I am using trjconv command to genrate the pdb structures.. trjconv_d -f md_0_1.trr -s md_0_1.tpr -o md_0_1.pdb -nice 0 -sep -skip 1000 -tu ns -b 1 -e 5000 error is coming"Fatal error: reading tpx file (md_0_1.tpr) version 73 with version 58 program. what is meaning of this error and wh

[gmx-users] hi

Hi all.. I want to ask if it is possible to restart the md run if due to power problem final md run not completed means initiating md from where is stop due to any reason? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: Re: [gmx-users] hi

thanx sarath 4r reply..can u expalin little bit more..I did not get from mdrun -h. On , Sarath Chandra Dantu wrote: On 29 May 2011 14:45, rashi.pari...@gmail.com> wrote: Hi all.. I want to ask if it is possible to restart the md run if due to power problem final md run not completed m

[gmx-users] query regarding g_ras command

I want to obtain solvent accessible surface area using g_sas command: g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.plz tell me the full command as i am getting error while running this command.thanx in advance!! how I will obtain three output files containing: area.xvg, resarea.xvg and atomarea.x

Re: [gmx-users] query regarding g_ras command

thanx justin..my problem is that i do not know exactly the syntax of command.i get to know about this command through this community only.i.e why i want the full command? On Tue, Jun 21, 2011 at 6:53 PM, Justin A. Lemkul wrote: > > > rashi parihar wrote: > >> I want

[gmx-users] error in running pdb2gmx command

HI all ..while running pdb2gmx command .I am getting error "Fatal error: Atom CT in residue TYR 314 was not found in rtp entry TYR with 20 atoms while sorting atoms" .what this error mean and how can I rectify this problem?plz help me. -- [image: images[12]] “Many Smiles Begin Because Of Anothe

Re: [gmx-users] error in running pdb2gmx command

(s) in your structure". Now my question is that how can i see or open the .rtp file of particular force field? On Wed, Jun 29, 2011 at 5:24 PM, Justin A. Lemkul wrote: > > > rashi parihar wrote: > >> >> HI all ..while running pdb2gmx command .I am getting error "Fatal

[gmx-users] regarding simulation of peptide and protein complex

Hello everyone.. I have 2 do the simulation of protein and peptide complex.I want to ask as for protein and ligand complex we have 2 create topology of ligand using prodrg sever mostly.Now if ligand is peptide then I have 2 build the topology of peptide using pdb2gx or anyother means?Looking forw