[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 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

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

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 wrong

[gmx-users] missing atoms

Hi All, I am running Gromacs for drug enzyme complex using AMBER as forcefield.While running pdb2gmx command I am getting error and warning of 790 missing atoms. Can anybody suggest me how to correct this error. error : --- WARNING: atom H

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

Dear ALL, I am running simulation for the drug enzyme complex using Gromacs with gromacs96(43a2)forcefield. After generating waterbox around my protein, when I am running grompp command (before energy minimization) I am getting following error:

[gmx-users] error:g_hbond

Dear All, I am running 20ns simulation of drug-enzyme complex using Gromacs software with GROMOS96 43a1 force field. After successful run when I am using g_hbond for the Hydrogen bond analysis I am getting following error.