RE: [gmx-users] amber DNA non-integer charge

Yes, you were right, upgrading it to 4.5.4 made sure the atom types/charges in the DNA termini were recognized correctly. This time the topology got generated with integer charges. thanks From: gmx-users-boun...@gromacs.org

Re: [gmx-users] OPLS-AA Unknown Atomtype

Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

[gmx-users] Phd positions available

Dear all, since many people in our group are gromacs users, this announcement could make some sense on the gmx mailing list. Please forward it to interested people. Best wishes, Giovanni Bussi ***PhD positions at SISSA in Physics and Chemistry of Biological Systems There are 3 positions

Re: [gmx-users] OPLS-AA Unknown Atomtype

Yao Yao wrote: Hi Justin, Thanks for your last reply. Now it seems that OPLS has known the atomtypes after I added those CA1, ... to ffoplsaanb.itp, but after I claim all the angles, dihedrals, ... in the ffoplsaabon.itp, it still gives errors like, Back Off! I just backed up mdout.mdp to

[gmx-users] Error found on grompp - energy minimization

Dear sir, I struck with the following error when i perform energy minimization. I unable to understand what did it mean? please make me clear. So kindly do the needful. Fatal error: Atomtype CR1 not found -- ** Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University,

Re: [gmx-users] Error found on grompp - energy minimization

On 29/08/2011 9:18 PM, ITHAYARAJA wrote: Dear sir, I struck with the following error when i perform energy minimization. I unable to understand what did it mean? please make me clear. So kindly do the needful. Fatal error: Atomtype CR1 not found One of your molecules is trying to use an

[gmx-users] Re: gromacs question topologie

Please keep all Gromacs-related correspondence on the gmx-users list, particularly if the discussion was previously carried out there. I am not a private tutor. Joschua Sterzenbach wrote: Hi is in the coordinate file only the geometry of the molecule? Yes. Have a look at its contents

[gmx-users] Re: Difficulty building a topology for a synthetic, branched PEG-peptide molecule [SOLVED]

That's a long bond. Does your reference length in specbond.dat suit it? IIRC there should be some evidence in the output of the special bond being formed if it actually is. If not, your symptoms are probably related Hi Mark, indeed, I think that was part of the problem. pdb2gmx indeed outputs a

[gmx-users] simulation at higher temperatures

Hi friends, As a part of my work i have to do simulation at higher temperature (400K or more) to study the folding, unfolding and stability of protein, for that i kept simulation for 3ns at 400k (400k temperature both in equilibration and production) keeping all the other parameters as usual

Re: [gmx-users] simulation at higher temperatures

arun kumar wrote: Hi friends, As a part of my work i have to do simulation at higher temperature (400K or more) to study the folding, unfolding and stability of protein, for that i kept simulation for 3ns at 400k (400k temperature both in equilibration and production) keeping all the

[gmx-users] g_lie

g_lie calculates the deltaG= alpha(Vl-s LJp - Vl-s LJw) + beta(Vl-s elp - Vl-s elw) equation. But when calculating DGbind from g_lie it will ask for only one term at a time i.e. -Elj for either Vl-s LJp or Vl-s LJw and -Cqq for either Vl-s elp or Vl-s elw. My question is when using only Vl-s LJp

Re: [gmx-users] OPLS-AA Unknown Atomtype

HI Justin, I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions. So I do not think ions addition will help. And I double-checked the angles, bonds, mentioned in the ffoplsaabon.itp, they are there. So I do not know any other files I may need

Re: [gmx-users] OPLS-AA Unknown Atomtype

Yao Yao wrote: HI Justin, I met these errors when I grompp to do 1st-time energy minimization before I planned to add the ions. So I do not think ions addition will help. And I double-checked the The net charge problem cannot be solved by adding ions. A fractional charge of that

[gmx-users] MARTINI / all-atom mapping

Hi all, I am trying to reverse-map some martini lipids to united atom. In order to do this, I'd prefer to have an EXACT definition of the aa-to-cg mapping. I cannot find this, only an imprecise graphic, in the MARTINI paper; the martini.itp file doesn't appear to list which heavy atoms are

[gmx-users] restarting a crashed job

Hello, My simulation crashed in the middle and I used the -cpi checkpoint.cpt -append option to continue. However, GROMACS cannot continue and complains about not being able to open the corresponding .trr file. I checked my folder, the trr file is there and the name is the same as the *.tpr and

Re: [gmx-users] restarting a crashed job

On 30/08/2011 1:14 PM, Payman Pirzadeh wrote: Hello, My simulation crashed in the middle and I used the /--cpi checkpoint.cpt --append/ option to continue. However, GROMACS cannot continue and complains about not being able to open the corresponding .trr file. I checked my folder, the trr