[gmx-users] protein covalently bond to ligand

Hi I want to do MD with a protien with prydoxal phosphate(PLP) which attache covalently to one lysine. For this I extract the Toplogy of lysine-PLP from PRODRG server.(DRGGMX.ITP and DRGPOH.PDB).I Changed the name DRGGMX.ITP to DRG.itp. after donig pdb2gmx -f m.pdb -o m1.pdb -water spce with th

[gmx-users] Atomtype '15.9994' not found

Hi I am doing md with protein-LYS-PLP (pyridoxal phosphate) which attach covalently. I could generate the DRG.itp, DRGPH.pdb files using PRODRG server. then merge DRG.itp in to the topol.top and DRGPH.pdb into the protein pdb file. When I use the grompp step before the energy minimization I en

[gmx-users] about do_dssp

Hi I have a question about do_dssp program.is it posible to define the amount of residus (the percentage) which have specific secondry structure, apart from the graphic file? if yes what is the the command? Thanks -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has bee

[gmx-users] protein domain separate

Hi I want to do MD on a two-domain protein (Protein A, Protein B). After doning position restranit for 20 ps, the final structure separated. How could I keep these 2 domain close to each other during whole MD run. Thank you in advance. -- Tehran University of Medical Sciences www.tums.ac.ir

[gmx-users] protein domain separate

Hi As I told in my perevious mail, My system consist of a 2-domain protein (Domain A and B), even when I did EM minimization this 2 damain separated. my em.mpf is: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integra

[gmx-users] protein domain separation

Hi I have done md simulation of a 2-domain protein in water, in 50 K but every time I did it these domains are separated from each other, and dont correct when I do trjconv -pbc nojump, previous time when I did em or pr by doing trjconv -pbc nojump, it corrected. The 50.mdp file is: title

[gmx-users] protein domain separate

Hi again I use -pbc mol -ur compact but the problem still exist. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users ma

[gmx-users] (no subject)

Subject: protein domain separate Date: Mon, 19 Oct 2009 08:56:36 +0430 Message-Id: <20091019042502.m55...@razi.tums.ac.ir> X-Mailer: OpenWebMail 2.53 20081220 334 X-OriginatingIP: 194.225.58.210 (hazizian) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Hi Tsjerk

[gmx-users] equilibtarion peiods for position restrain

hi How could we test that the protein + solvent come to equilibration after position restrain job. my protein have 322 residue and I don't konw how much time the equilibtarion peiods should be? thank's. -- Tehran University of Medical Sciences www.tums.ac.ir ___

[gmx-users] equilibtarion peiods for position restrain

hi how could we test that the protein + solvent come to equilibration after position restrain job. my protein have 322 residue and I don't konw how much time the equilibtarion peiods should be? thank's. -- Tehran University of Medical Sciences www.tums.ac.ir ___

[gmx-users] Pr reach and not reach to equilibria

Hi gromacs users I have done Position restrain for 50 ps. after it had finished, I checked the rmsd for confident that rms reached to it's equilibrate mode. When I check it by g_rms command and select system subgroup, I find that it had not reached to equilibria, but after I check It by p

[gmx-users] error in parallel mdrun

hi I want to use mdrun, when i use It as one job it goes on. but when i use as parallel job > grompp -np 4 -f md300.mdp -c pr.pdb -p topol.top -o md300.tpr > then > mpirun -np 4 mdrungromacs_mpi -nice 0 -v -s md300.tpr -o md300.trr -c md300.pdb -e md300.edr -g md300.log

[gmx-users] mdrun parallel problem

hi when I run mdrun command every thing is Ok and the mdrun go ahead. but when I use mpimdrun -np 4 mdrungromacs_mpi (parallel mode) for that system this error ocurres: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max inf (between atoms 10 and 13) rms nan bonds t

[gmx-users] mdrun mpi problem

Hi I have 3 computer and I want to do mdrun_mpi. I define this system in hostfile, lambhost-def, lam-hostmap.txt after lamboot and lamnodes It defines me that I have 3 nodes: h...@dma210:~/etc> lamnodes n0 dma210.dma:2:origin,this_node n1 dma211.dma:2: n2 dma212.dma:2: then I do:

[gmx-users] problem in analyzing

Hi I want to analyze md. This md took 10 ns(1 ps) for a protein with 206 residue and 2 Mn plus about 17000 molecule solvent as water. then I construct extra group containig Protein+2 Mn with make_ndx comand. I did g_rmsf for extracting the average structure of the new group rmsd equilibrated

[gmx-users] the reson for neutralizing the charge

Hi my ligand is Arginine (so it is not neccessary to use PRODRG )and the OPLS forcefield of gromacs make the itp file of it. I check and all the atoms present in the ligand itp file.There is no missing atom in the file. atoms ] ; nr type resnr residue atom cgnr charge mas

[gmx-users] the reson for neutralizing the charge

Hi Justin and all Thak you very much my problem solve. -- Tehran University of Medical Sciences www.tums.ac.ir -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ gmx-users mailing list