[gmx-users] converting all-atom pdb to cg.pdb

Does the atom2cg_v2.1.awk require the indication of the subunit (A, B, C, etc) in the pdb file of a multimeric protein? From ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00 N ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00 0.00 C ATOM 3

Re: [gmx-users] converting all-atom pdb to cg.pdb

Francesco Pietra wrote: Does the atom2cg_v2.1.awk require the indication of the subunit (A, B, C, etc) in the pdb file of a multimeric protein? From ATOM 1 N LEU 1 153.242 64.673 95.851 0.00 0.00 N ATOM 2 CA LEU 1 154.534 64.963 95.169 0.00

Re: [gmx-users] Problem with topolbuild

On Sun, November 8, 2009 at 5:31:30 PM, Gunnar Widtfeldt Reginsson regins...@gmail.com wrote: I have a small organic molecule that I processed with antechamber using the gaff forcefield and got a mol2 file. I want to get .gro and. itp files from this to use with GROMACS. So I tried to use the

Re: [gmx-users] Can not find forcefield for atom C4-1 with 0 bonds

Darrell Koskinen wrote: Hi, I am trying to create a topology file from a .gro file. When I run x2top with methane (C4 opls_066) in my .gro file, I receive the following warning: /Can not find forcefield for atom C4-1 with 0 bonds/ I have included the following line in the ffoplsaa.n2t

Re: [gmx-users] Problem with topolbuild

Thank you. I am new to Unix commands, so could you please explain a little more how I am to apply these bug fixes? Thanks On Mon, Nov 9, 2009 at 12:51 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Sun, November 8, 2009 at 5:31:30 PM, Gunnar Widtfeldt Reginsson regins...@gmail.com wrote:

Re: [gmx-users] g_energy

Thanks allot for the ultrafast response and above all your help !. Arik Mark Abraham wrote: Arik Cohen wrote: Hi, Is there a way to tell the g_energy program the output option(i.e. Potential, Temperature ) in advance when you run the program. Namely, I would like to know if there is a

Re: [gmx-users] Problem with topolbuild

On Mon, November 9, 2009 at 8:14:29 AM, Gunnar Widtfeldt Reginsson regins...@gmail.com wrote: Thank you. I am new to Unix commands, so could you please explain a little more how I am to apply these bug fixes? For short patches like these, I just use a text editor. Because the mailing list

[gmx-users] Free energy calculations

I'm interesting to calculate Gibbs energy using g_lie application. Unfourtunately, I don't know what kind of state equation is the sub-program using. Can you help me with that. Best regards Jorge R. Quintero Grupo de Investigación en Fisicoquímica Teórica y Experimental Universidad Industrial

Re: [gmx-users] S-type Hydrogen bond correlation function

I commented out the 'read_next_x' routine and in place of it i added 'read_next_frame' as given below will that work? Now if i install will i get the trajectory? Is API available for gromacs? Thank you. write_trx(out,natoms,swi,top.atoms,0,t,box,x,NULL); } /* }

[gmx-users] MD with bilayer

Hi I have constructed the bilayer with protein molecule in VMD. Can any one tell how to start MD from here. the initial step - pdb2gmx is not working for this complex(pdb+membrane) thanks in advance Parthiban -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Problem with topolbuild

It works. Thank you so much. Regards, Gunnar W. On Mon, Nov 9, 2009 at 4:26 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Mon, November 9, 2009 at 8:14:29 AM, Gunnar Widtfeldt Reginsson regins...@gmail.com wrote: Thank you. I am new to Unix commands, so could you please explain a little

Re: [gmx-users] MD with bilayer

Hi, VMD was built to work with NAMD, so the atom names and topologies will not work with GROMACS. I guess you better go to Peter Tieleman site ( http://moose.bio.ucalgary.ca/) and rad there how to do things. Cheers, Itamar On Tue, Nov 10, 2009 at 8:05 AM, Mark Abraham

Re: [gmx-users] MD with bilayer

parthi...@ncbs.res.in wrote: Hi I have constructed the bilayer with protein molecule in VMD. Can any one tell how to start MD from here. Follow the methods of whichever tutorial you learned from :-) the initial step - pdb2gmx is not working for this complex(pdb+membrane) We're not

Re: [gmx-users] S-type Hydrogen bond correlation function

Ramachandran G wrote: I commented out the 'read_next_x' routine and in place of it i added 'read_next_frame' as given below will that work? You could try it, but it won't work. The whole do...while loop needs to be adjusted to use fr and its struct members, rather than separate box, t, x,

[gmx-users] Missing H from residue

I tried to protonate my pdb file using openbabel babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h Then I ran pdb2gmx with the following pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh But apparently I am missing a H from my first residue. Is there

Re: [gmx-users] Missing H from residue

Well I was just wondering if there was some porgram that could add this atom automatically. It looks like this H is missing. I supposed I could re-write the pdb file. It has all these non-standard Hydrogens. HB, HG and HT. Maybe I can just replace those. This is the residue in question ATOM

Re: [gmx-users] Missing H from residue

Jack Shultz wrote: I tried to protonate my pdb file using openbabel babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h Then I ran pdb2gmx with the following pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p Protein.top -water spce -ignh But apparently I am missing a H from my

Re: [gmx-users] Missing H from residue

Jack Shultz wrote: Well I was just wondering if there was some porgram that could add this atom automatically. It looks like this H is missing. I supposed I could re-write the pdb file. It has all these non-standard Hydrogens. HB, HG and HT. Maybe I can just replace those. Non-standard?

Re: [gmx-users] Free energy calculations

Can you be more specific in the question of what property you want to compute for which molecule or molecules? Linear Interaction energy approaches are not always very efficient for coulomb, and is definitely not exact for the LJ term. So LIE might not be what you want to be doing. Michael

Re: [gmx-users] Missing H from residue

I modified the N-Terminal and C-Terminal Residues. [boinc...@vps test]$ grep NGLU ProteinAmber.pdb grep CARG ProteinAmber.pdb ATOM 1 N NGLU 32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA NGLU 32 -19.847 8.507 -3.304 1.00 0.00 C ATOM 3 C

Re: [gmx-users] Missing H from residue

Jack Shultz wrote: I modified the N-Terminal and C-Terminal Residues. [boinc...@vps test]$ grep NGLU ProteinAmber.pdb grep CARG ProteinAmber.pdb ATOM 1 N NGLU 32 -20.050 8.920 -4.700 1.00 0.00 N ATOM 2 CA NGLU 32 -19.847 8.507 -3.304 1.00 0.00 C

Re: [gmx-users] Missing H from residue

Jack Shultz wrote: snip --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry with 25 atoms while sorting atoms

Re: [gmx-users] Missing H from residue

On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: snip --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not found in rtp entry

Re: [gmx-users] Missing H from residue

Jack Shultz wrote: On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: snip --- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom O in residue CARG 244 not

Re: [gmx-users] Missing H from residue

Thanks Justin! Got it now. On Mon, Nov 9, 2009 at 10:00 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Jack Shultz wrote: snip --- Program

[gmx-users] Please tell me how to simulate two structures together in a water box

Respected Sir, Please tell me how to simulate two different stuctures together in a water box so as to have an idea of drug docking and what options to use. Any suggestions are welcome. With Regards Radhika Connect more, do more and share more with Yahoo! India Mail. Learn more.

[gmx-users] (no subject)

After installing gromacs4.0 on windows it created Gromacs directory containing several .exe files in bin directory. But when I used pdb2gmx command it will shows that basch command is not found. So anyone can tell me what is that. -- Pawan Kumar Raghav Bioinformatician Stem Cell and Gene

Re: [gmx-users] (no subject)

pawan raghav wrote: After installing gromacs4.0 on windows it created Gromacs directory containing several .exe files in bin directory. But when I used pdb2gmx command it will shows that basch command is not found. So anyone can tell me what is that. See point 8 here

Re: [gmx-users] Please tell me how to simulate two structures together in a water box

radhika jaswal wrote: Respected Sir, Please tell me how to simulate two different stuctures together in a water box so as to have an idea of drug docking and what options to use. Any suggestions are welcome. Your question is too general. If you need help with GROMACS workflows, you should

[gmx-users] topology file in .dat format

Hello I have a gromos96 topology file for a ligand and it is in xx.dat format.How do I include this file in my gromacs version 4.0 simulation of a protein? Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing list

Re: [gmx-users] topology file in .dat format

Hi Subarna, There is no .dat format for topologies. It may be named .dat, but the inside (format) is what matters. If you're confident it is gromos96 format, you can #include it the same way as other molecule definition topology files. Do mind that there's quite a difference between GROMOS96