Re: [gmx-users] pdb2gmx error

Ilya Chorny wrote: I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to the side chain nitrogen called ASBG. I want to test the new residue by itself. When I pdb2gmx it I get the following error. --- Program pdb2gmx,

[gmx-users] pdb2gmx error

I created a new ffoplsaa.rtp entry for ASN with a polysacharide attached to the side chain nitrogen called ASBG. I want to test the new residue by itself. When I pdb2gmx it I get the following error. --- Program pdb2gmx, VERSION 4.0.3 Source code

Re: [gmx-users] how to parametrize Phos. Thr TPO

There is already a user contribution in the gromacs page named ffG43a1p, that is based in the force field ffG43a1 and also includes phosphorilated serine end threonine. However, is exciting doing it for yourself. Mensaje citado por nahren manuel : > Dear Gromacs Users, > > I am trying to simulate

Re: [gmx-users] using more than one type of molecules

Justin A. Lemkul wrote: Molecular Dynamics wrote: Dear Justin, I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the PRODRG. And you suggested that ' If these come from PRODRG, they will probably require manual modification and validation of their contents.' What kind of mo

Re: [gmx-users] using more than one type of molecules

Molecular Dynamics wrote: Dear Justin, I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the PRODRG. And you suggested that ' If these come from PRODRG, they will probably require manual modification and validation of their contents.' What kind of modifications should I do ? C

Re: [gmx-users] how to parametrize Phos. Thr TPO

nahren manuel wrote: but i get the following error * * * * * Generated 380 of the 1326 non-bonded parameter combinations ERROR 0 [file "top_A.itp", line 16530]: No default Proper Dih. types ERROR 0 [file "top_A.itp", line 16531]: No default Proper Dih. types Then you haven't a

Re: [gmx-users] ion jump out of protein

Homa Azizian wrote: Hi I mean after MD the ion was not in the active site, the location of ion is out of the protein. Then your model physics is wrong and you will have to re-think/re-derive appropriate parameters. -Justin My ion jump out of the protein after MD.My ion (MN) has not any

Re: [gmx-users] using more than one type of molecules

Dear Justin, I use DRGGMX.ITP and DRGPOH.PDB for each type of molecule from the PRODRG. And you suggested that ' If these come from PRODRG, they will probably require manual modification and validation of their contents.' What kind of modifications should I do ? Could you please give me some in

[gmx-users] ion jump out of protein

Hi I mean after MD the ion was not in the active site, the location of ion is out of the protein. > My ion jump out of the protein after MD.My ion (MN) has not any covalant > bond by its neibour, just has electrostatic intraction. > is there any line that I have to add to the itp file or top f

[gmx-users] how to parametrize Phos. Thr TPO

Dear Gromacs Users, I am trying to simulate a protein whose Thr residues is phosphorylated. I did the following based on the earlier query regarding the same here is how I did it for phosphorylated Threonine. 1) open the appropriate .rtp file e.g. ffG43a1.rtp 2) make a copy of the exi

Re: [gmx-users] (no subject)

Hello. What do you mean by "jump"? Perhaps the "connected MN" is a stable state? If you'll supply more details we could try to help you better. --Omer. On Sat, Mar 14, 2009 at 08:15, Homa Azizian wrote: > My ion jump out of the protein after MD.My ion (MN) has not any covalant > bond by its neibo

Re: [gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."

xiaowu...@hotmail.com wrote: > Dear, > As a small test, I want to simulate polystyene(PS) using GROMACS. > Firstly, I obtain a pdb file of a PS chain consisting of 20 repeating > unit(320 atoms totally ) and add the STY residues to the .rtp files. > while running pdb2gmx, the procedure was fin

Re: [gmx-users] Energy/temperature drifts in Gromacs 4.0 / inconsistencies with Gromacs 3.3.1

Pietro Amodeo wrote: ADDENDUM: I've just compiled Gromacs 3.3.3 on cluster NEW, with Intel compiler (see below). A simulation (still running) on system 2 with the paralled double-prec version shows preliminary results in line with gromacs 3.3.1 on cluster OLD, with no trace of abnormal oscillatio

[gmx-users] "Now there are 16 atoms. Deleted 304 duplicates."

Dear, As a small test, I want to simulate polystyene(PS) using GROMACS. Firstly, I obtain a pdb file of a PS chain consisting of 20 repeating unit(320 atoms totally ) and add the STY residues to the .rtp files. while running pdb2gmx, the procedure was finished "successfully". but I find that o

Re: [gmx-users] Triclinic water box for a protein MD

You're welcome. Forgot to mention that it comes with an additional .mdp option (rototr = yes/no). That does break compatibility with other versions regarding reading .tpr files. Cheers, Tsjerk On Fri, Mar 13, 2009 at 10:48 PM, TJ Piggot wrote: > This looks great thanks, had meant to try and imp