[gmx-users] DSSP and g_sas

Which among DSSP and g_sas is better for calculating solvent accessible surface area of proteins? -- Bhanu Prakash. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting

Re: [gmx-users] problem in dna-protein simulation

Edit your pdb as per ur rtp file / forcefield. On 16/06/2009, Justin A. Lemkul jalem...@vt.edu wrote: nitu sharma wrote: Dear all, i am trying to simulation of dna-protein complex using gromacs with amber port . I am using amber99 port with gromacs-4.0.3 version. I am

[gmx-users] Strange error in DNA simulations..

-- -[no]h bool no Print help info and quit -niceint0 Set the nicelevel -deffnm string bhanu Set the default filename for all file options -[no]xvgrbool yes Add specific codes (legends etc

Re: [gmx-users] Strange error in DNA simulations..

On 15/06/2009, Mark Abraham mark.abra...@anu.edu.au wrote: On 06/15/09, *Bhanu *bhanui...@gmail.com wrote: Hi Group, I've tried simulating a five bp dna. It has showed many atoms missing and some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and -mising options. Later

Re: [gmx-users] Strange error in DNA simulations..

Hi, I didn't ignore your link, I was trying all things suggested in wiki.. Its the greed for more and more suggestions made me to type those.. Anyway, thanks for the link, buddy! On 15/06/2009, Mark Abraham mark.abra...@anu.edu.au wrote: On 06/15/09, *Bhanu *bhanui...@gmail.com wrote

Re: [gmx-users] Failing installation with --enable-mpi option

Dear Justin, could you please write what environmental changes you made to MPICC.. I tried to alter the profile, but it is rejecting all of them.. Bhanu. On 20/05/2009, Bhanu bhanui...@gmail.com wrote: Thanks Justin, will try your suggestion.. 2009/5/20 Justin A. Lemkul jalem...@vt.edu

[gmx-users] Failing installation with --enable-mpi option

I tried to install Gromacs on my Core2Quad pc with the command ./configure --enable-mpi --disable-nice --program-suffix=_mpi it is showing the following error result: [sand...@bhanu gromacs-4.0.3]$ ./configure --enable-mpi --disable-nice --program -suffix=_mpi checking build system type

Re: [gmx-users] Failing installation with --enable-mpi option

Thanks Justin, will try your suggestion.. 2009/5/20 Justin A. Lemkul jalem...@vt.edu: Bhanu wrote: I tried to install Gromacs on my Core2Quad pc with the command  ./configure --enable-mpi --disable-nice --program-suffix=_mpi it is showing the following error result: [sand...@bhanu

Re: [gmx-users] How can i know if the protein swell during the MD simulation?

How about checking radius of gyration??? 2009/5/18 Tsjerk Wassenaar tsje...@gmail.com Hi, Well, I think 'swelling' is unambiguously, though roughly, defined as 'growing larger', which suggests that you'd have to look for an increase in volume. But how to do that, how to define the volume of

[gmx-users] Genion failing in parallel runs.

Hi, I'm using Gromacs 3.3.3, installed with double precision. When I run genion with this command: genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral the following error message was generated: Program

Re: [gmx-users] protein/dmso simulation

Try genbox -cp *.gro -ci dmso.gro -p *.top -o *.gro Gro file for dmso comes built-in with gromacs 3.3. As Justin has directed, forcefields do matter. On 19/08/2008, Justin A. Lemkul [EMAIL PROTECTED] wrote: prasun kumar wrote: dear users I am trying to run the simulation fo a protein/DMSO

[gmx-users] Protein is moving out of box.

Hi all, am new to Gromacs. I tried a 10 ps simulation with a protein and after the run, the protein came out of the box.. is it good or bad? How can I keep the protein in the box? Waiting for ur reply. Bhanu. -- _ _ (_)(_) (,,) =()= ((__)\ _|L\___/ The Lab Rats