[gmx-users] FATAL ERROR: Residue "LIG" not found in residue topology database.

Dear All usres: I am trying to do a simple system that contains 4 molecules ethane and MD run using GROMACS. I build my .pdb file by using Avogadro software . Afterwards, I try to generate the topology and .gro file using pdb2gmx program and it generates an error. I am using the 43a1 force field.

Re: [gmx-users] FATAL ERROR: Residue "LIG" not found in residue topology database.

On 7/31/12 7:48 AM, Ali Alizadeh wrote: Dear All usres: I am trying to do a simple system that contains 4 molecules ethane and MD run using GROMACS. I build my .pdb file by using Avogadro software . Afterwards, I try to generate the topology and .gro file using pdb2gmx program and it generates

[gmx-users] FATAL ERROR Residue "LIG" not found in residue topology database?

Dear All usres: I am trying to do a simple system that contains 4 molecules ethane and MD run using GROMACS. I build my .pdb file by using Avogadro software . Afterwards, I try to generate the topology and .gro file using pdb2gmx program and it generates an error. I am using the 43a1 force field.

[gmx-users] make_ndx: duplicates groups appearing in index.ndx file

Hello, I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm having an issue with make_ndx. Using the old version I have a single group showing up for each "odd" residue, eg JJJ shows up once as group 16 for example. When I use the new version on the same file I get 2 groups a

Re: [gmx-users] make_ndx: duplicates groups appearing in index.ndx file

On 7/31/12 10:14 AM, Laura Kingsley wrote: Hello, I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm having an issue with make_ndx. Using the old version I have a single group showing up for each "odd" residue, eg JJJ shows up once as group 16 for example. When I use the new

[gmx-users] Isothermal compressibility for polymers - regd

Dear GMX users, How one can calculate Isothermal compressibility for given system ( eg : Materials like polymers ) using gromacs. Thank you in advance. Regards, Ramesh Cheerla. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/lis

[gmx-users] Double X Simple precision

Hi folks! I'm running Gromacs in double precision to minimize my system until 10^-4 kcal/mol.nm 'cause it's too much unstable. Unfortunately, my system is huge and double precision make the simulation slower. My question is: can I run minimization process in double precision and simulation itself

[gmx-users] Re: Double X Simple precision

marcelodepolo wrote > > I'm running Gromacs in double precision to minimize my system until 10^-4 > kcal/mol.nm 'cause it's too much unstable. Unfortunately, my system is > huge and double precision make the simulation slower. > > My question is: can I run minimization process in double precisio

[gmx-users] Molecule in topology has atom numbers below and above natoms

Hello Everybody I'm running a production simulation of a kinase (after minimization and equilibration) and after concluded 20ns I got the following problem when I tryied to run g_rmsf "Fatal error: Molecule in topology has atom numbers below and above natoms (4005). You are probably trying to use

[gmx-users] Re: Molecule in topology has atom numbers below and above natoms

Thales Kronenberger wrote > > Hello Everybody > > I'm running a production simulation of a kinase (after minimization > and equilibration) and after concluded 20ns I got the following > problem when I tryied to run g_rmsf > > "Fatal error: > Molecule in topology has atom numbers below and above

Re: [gmx-users] Diagnosing + system blowing up

Thanks for dear Mark's suggestions. What's the typical solution to fix such errors of grompp? I don't have any idea to do what, so erased the lines defined in output of grompp, then I went through the NVT equilibrium, it didn't stop by multiple interaction errors. I don't know what will happen f

Re: [gmx-users] Diagnosing + system blowing up

On 7/31/12 5:21 PM, Shima Arasteh wrote: Thanks for dear Mark's suggestions. What's the typical solution to fix such errors of grompp? I don't have any idea to do what, so erased the lines defined in output of grompp, then I went through the NVT equilibrium, it didn't stop by multiple intera

Re: [gmx-users] Diagnosing + system blowing up

 All right. Thanks. Sincerely, Shima - Original Message - From: Justin Lemkul To: Shima Arasteh ; Discussion list for GROMACS users Cc: Sent: Wednesday, August 1, 2012 2:04 AM Subject: Re: [gmx-users] Diagnosing + system blowing up On 7/31/12 5:21 PM, Shima Arasteh wrote: > Tha

[gmx-users] Re: Diagnosing + system blowing up

Shima Arasteh wrote > > Thanks for dear Mark's suggestions. > > What's the typical solution to fix such errors of grompp? > As I've said lots of times, you need to go and look at the atom types you're using, what interactions are defined for them in ffbonded.itp and perhaps reassess those type

Re: [gmx-users] Re: Diagnosing + system blowing up

Thanks so much. OK. I'll do my best.   Sincerely, Shima - Original Message - From: Mark Abraham To: gmx-users@gromacs.org Cc: Sent: Wednesday, August 1, 2012 2:49 AM Subject: [gmx-users] Re: Diagnosing + system blowing up Shima Arasteh wrote > > Thanks for dear Mark's suggestions. >

Re: [gmx-users] Re: Diagnosing + system blowing up

 But If I want to use acetyl instead of formyl, then what about the chemical activity of the formyl located in N-terminus? The protein that I will put in the bilayer is composed of 2 monomers . The monomers form a dimer from the N-terminus, the same as gramicidin A channel. Acetyl could be pl

Re: [gmx-users] Re: Diagnosing + system blowing up

On 7/31/12 7:46 PM, Shima Arasteh wrote: But If I want to use acetyl instead of formyl, then what about the chemical activity of the formyl located in N-terminus? The protein that I will put in the bilayer is composed of 2 monomers . The monomers form a dimer from the N-terminus, the same

[gmx-users] A Force Field Paper including Heme Proteins

Dear gromacs users, We just published a paper titled "Force field development for cofactors in the photosystem II" in Journal of Computational Chemistry, which includes the Amber03 compatible force field for heme-B and works well with heme proteins. You may use it for reference at your convenienc

[gmx-users] Fatal error: Number of grid cells is zero. Probably the system and box collapsed.

Dear gromacs user I did simulation of carbon nanotube (one in center and 6 in the vicinity of that)|: every CNT have 120 atoms. 1) energy minimization 2) equilibration in NVT ensemble when I did equilibration in NPT ensemble, I encountered Fatal error: Number of grid cells is zero. Probably the

Re: [gmx-users] Fatal error: Number of grid cells is zero. Probably the system and box collapsed.

On 1/08/2012 1:06 PM, leila karami wrote: Dear gromacs user I did simulation of carbon nanotube (one in center and 6 in the vicinity of that)|: every CNT have 120 atoms. 1) energy minimization 2) equilibration in NVT ensemble when I did equilibration in NPT ensemble, I encountered Fatal error