Re: [gmx-users] x2top & Library file ffG43a1.n2t

[EMAIL PROTECTED] wrote: Hi all, I have been trying to generate .rtp, .top files from having input of .gro file for particular molecule in gromacs. I tried this with (x2top) command implemented in gromacs but i have encountered a problem while executing this command , that i am mentioning below.

Re: [gmx-users] (no subject)

[EMAIL PROTECTED] wrote: Hi all, I have been trying to generate .rtp, .top files from having input of .gro file for particular molecule in gromacs. I tried this with (x2top) command implemented in gromacs but i have encountered a problem while executing this command , that i am mentioning below.

[gmx-users] x2top & Library file ffG43a1.n2t

Hi all, I have been trying to generate .rtp, .top files from having input of .gro file for particular molecule in gromacs. I tried this with (x2top) command implemented in gromacs but i have encountered a problem while executing this command , that i am mentioning below. Fatal error: Library file

[gmx-users] (no subject)

Hi all, I have been trying to generate .rtp, .top files from having input of .gro file for particular molecule in gromacs. I tried this with (x2top) command implemented in gromacs but i have encountered a problem while executing this command , that i am mentioning below. Fatal error: Library file

Re: [gmx-users] Asking help about PME

shall you find them yourself first? /src/mdlib/*fft* Actual FFT is done by FFTW. Regards, Yang Ye xuji wrote:

Re: [gmx-users] Asking help about PME

xuji wrote: > > Hi all gromacs users: > > I am digging into the PME method in gromacs. Can someone tell > me what files have something to do with PME and the corresponding > method FFT? >From the gromacs source directory, try find * -name "*pme*" and grep -i pme src/*/*.c include/*.h include

[gmx-users] Asking help about PME

Hi all gromacs users: I am digging into the PME method in gromacs. Can someone tell me what files have something to do with PME and the corresponding method FFT? Thanks! 　　 Best wishes! Ji Xu Institute of Process Engineering Chinese Academy of Sciences P.O.Box 353, Beijing, 100080, China Tel

Re: [gmx-users] Re: Targeted MD

Steven Kirk wrote: Mark Abraham <[EMAIL PROTECTED]> wrote "Non-Protein" serves well here. So a usual tc-grps line has "Protein Non-Protein" for a protein simulation. Mark A supplementary question. The tc-grps line can take predefined standard group names such as 'System', 'Protein' and '

Re: [gmx-users] do_dssp file format

ABEL Stephane 175950 wrote: I used the following command ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault. Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and

[gmx-users] do_dssp file format

I used the following command ./do_dssp -s test.SecStruc.tpr with test.SecStruc.tpr is a pdb file with a part is show below. I obtained a segmentation fault. Maybe it is not a the good command. Remember that my trajectories are not made/compatible with GROMACS and i have only a pdb coordinat

Re: [gmx-users] Dihedral with parameters set to zero

Hmmm, thanks. An obvious solution, but I had not yet thought of that myself. Well, you know what they say: Een dag niets geleerd is een dag niet geleefd! ;-) >Date: Thu, 10 Jan 2008 19:27:38 +0100 >From: David van der Spoel <[EMAIL PROTECTED]> >Subject: Re: [gmx-users] Dihedral with parameters s

Re: [gmx-users] Re: gmx-users Digest, Vol 45, Issue 30

Prasad Gajula wrote: Dear Dr. David, Thank you very for the reply. When i looked the energy minimized average structure it looks just fine. ?? but you did not say energy minimized... check the rmsd between average and minimized average structure as well. Maybe you want to do a clustering analy

[gmx-users] Re: gmx-users Digest, Vol 45, Issue 30

Dear Dr. David, Thank you very for the reply. When i looked the energy minimized average structure it looks just fine. ?? >>> >> I calcualted the average structure from the simulation trajectory. when >> I >> calculate the rmsd of the protein to this average sturture, it is giving >> average rmsd

Re: [gmx-users] rmsd with average structure

Prasad Gajula wrote: Dear Groamcs users, I calcualted the average structure from the simulation trajectory. when I calculate the rmsd of the protein to this average sturture, it is giving average rmsd of 0.16 nm. But, it is not clear for me why the average sturcture is never adapted rmsd near (o

[gmx-users] rmsd with average structure

Dear Groamcs users, I calcualted the average structure from the simulation trajectory. when I calculate the rmsd of the protein to this average sturture, it is giving average rmsd of 0.16 nm. But, it is not clear for me why the average sturcture is never adapted rmsd near (or equal) to zero. I did

[gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

When actually building the topology I find it easiest to create the residues in the relevant .rtp and allow pdb2gmx to build the topology for you. However, all this does is correctly connect everything and put your parameters where they should be. All previous comments (in this thread and the h

Re: [gmx-users] Dihedral with parameters set to zero

van Bemmelen wrote: OK. Now I'm confused. What did you mean by the second part? Of course, when doing FEP with the B state different, you would gradually introduce a dihedral as lambda increases. But that would still mean that setting all dihedral parameters to 0 for the A state would be exactly

Re: [gmx-users] do_dssp file format

Quoting ABEL Stephane 175950 <[EMAIL PROTECTED]>: > > Hi gromacs users > > > > For my work I have performed some simulations of a protein in water with an > other MD software not compatible with >GROMACS. And I would like to compute > the time evolution of the secondary structure of my protein, I

Re: [Bulk] Re: [gmx-users] Re: Targeted MD

Protein are defined by the residue names inside aminoacids.dat. So, it is possible for nucleic acid to be "Protein". Steven Kirk wrote: Mark Abraham <[EMAIL PROTECTED]> wrote Subject: Re: [gmx-users] Re: Targeted MD To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Conten

RE: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

Hi Soni, I have never had such problems, but only some suggestions: 1) Try the PRODRG beta server (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta) 2) Try drawing your molecule (or part of it) directly with the JME editor, included on the PRODRG website 3) Try using another input file type,

[gmx-users] RE: gmx-users Digest, Vol 45, Issue 28

Hi Soni, I have never had such problems, but only some suggestions: 1) Try the PRODRG beta server (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta) 2) Try drawing your molecule (or part of it) directly with the JME editor, included on the PRODRG website 3) Try using another input file type,

Re: [gmx-users] Dihedral with parameters set to zero

OK. Now I'm confused. What did you mean by the second part? Of course, when doing FEP with the B state different, you would gradually introduce a dihedral as lambda increases. But that would still mean that setting all dihedral parameters to 0 for the A state would be exactly equivalent to having

Re: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

Mufaddal Soni wrote: Dear users, I am working with PTP1B protein. Recently I tried to run it in gromacs along with an inhibitor {[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN- 2-YL]-DIFLUORO-METHYL}-PHOSPHONIC ACID[FNP in short]. The problem is that gromacs does not recogniz

[gmx-users] use do_dssp with only pdb file with many configurations in it

Hi gromacs users In previous message Mark Abraham. said me that do_dssp tools can be used only with a pdb file (thank to him ;))). I am newbie with gromacs (i came from the ORAC MD world), so i have two questions 1 °) Can do_dssp can be used with "only" one pdb file with some configurations

[gmx-users] do_dssp file format

> Hi gromacs users > > For my work I have performed some simulations of a protein in water with an > other MD software not compatible with >GROMACS. And I would like to compute > the time evolution of the secondary structure of my protein, I know that the > >with >the xpm2ps tool give in gromacs

Re: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

Quoting Mufaddal Soni <[EMAIL PROTECTED]>: > Dear users, > I am working with PTP1B protein. Recently I tried to run it > in gromacs along with an inhibitor > {[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN- 2-YL]-DIFLUORO-METHYL}-PHOSPHONIC > ACID[FNP in short]. The problem is that

Re: [gmx-users] Re: Targeted MD

Mark Abraham <[EMAIL PROTECTED]> wrote Subject: Re: [gmx-users] Re: Targeted MD To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=ISO-8859-1; format=flowed wei-xin xu wrote: > Some hints on practices that generally *not a good idea* to us

Re: [gmx-users] g_covar

Mark Abraham wrote: tangxuan wrote: Mark Abraham wrote: tangxuan wrote: Thanks for your reply. I have another question. I can get the coordinates covariance by option -ascii, but do you know how to get a exact covariance value for each atom? How do you mean "exact", and in what format? Ma

[gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.

Dear users, I am working with PTP1B protein. Recently I tried to run it in gromacs along with an inhibitor {[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN- 2-YL]-DIFLUORO-METHYL}-PHOSPHONIC ACID[FNP in short]. The problem is that gromacs does not recognize FNP and hence I am no

Re: [gmx-users] g_covar

tangxuan wrote: Mark Abraham wrote: tangxuan wrote: Thanks for your reply. I have another question. I can get the coordinates covariance by option -ascii, but do you know how to get a exact covariance value for each atom? How do you mean "exact", and in what format? Mark __

Re: [gmx-users] Pi Stacking in OPLSAA ff

Ramya Cherukupalli wrote: Dear all, I am trying to simulate a mutant lipase molecule using OPLS AA forcefield. In the crystal structure study, presence of a Pi-stacking interaction has been proposed to help in enhancement of thermostable behavior of the mutant. I wanted to clarify 2 things.

[gmx-users] Pi Stacking in OPLSAA ff

Dear all, I am trying to simulate a mutant lipase molecule using OPLS AA forcefield. In the crystal structure study, presence of a Pi-stacking interaction has been proposed to help in enhancement of thermostable behavior of the mutant. I wanted to clarify 2 things.. 1. Does OPLS AA paramete

Re: [gmx-users] g_covar

Mark Abraham wrote: tangxuan wrote: Thanks for your reply. I have another question. I can get the coordinates covariance by option -ascii, but do you know how to get a exact covariance value for each atom? How do you mean "exact", and in what format? Mark ___