[gmx-users] Re:mdrun_problem

Hi users, I am having a problem during the running of the mdrun program on my prepared system.I have a system containing a protein/peptide complex. i have prepared the protein using the pdb2gmx utility and the peptide using the PRODRG utility. I have then included the ligand .itp file into the pro

[gmx-users] Re:mdrun_problem

Mark and other users, Thanks for the input. I understand that translation does not have any effect on the energy calculations since the point of reference is the protein itself. The problem over here is that if a translation operation is to be done it should perform the same operation on all the

[gmx-users] mdrun_problem

Hello users, I am trying to check wether my prepared system is ready to be put into a simualtion. I have a 2 body system 1protein + 1peptide. I have prepared the peptide using PRODRG server and included it into the protein .top file. I wanted to do a dummy minimization run with my prepared prote

[gmx-users] Atomtype:CB

Hello users, I found a problem similar to one described in the mailing list. The problem occurs in grompp wherein it says unrecognized atom type CB. As suggested in the mailing list the problem arises when in a ligand protein system the ligand is prepared using the PRODRG server GROMOS87 format

[gmx-users] charge_calculation

Hello users, I want to implement the charges calculated using the gaussian/chelpg method for my ligand for a simulation. I have done the calculations and substituted the relevant charges in the .itp file of the ligand. I was wondering wether i should change the cgnr number to a single value o

[gmx-users] Solvent_box

Hi, Sorry for the inconvenience caused. The output from the script suggests that the pdb file is written. However when i open the pdb file the solvent box is not created in full. Since i could not provide the structure on the mailing list it was a bit difficult for the other person to comprehend

[gmx-users] Solvent_box

Hi users, To answer Mark's question about reading section 3.2. Yes I have.I wish to conduct an SMD study.I want to place my protein system at one end of the longest side of triclinic shell and then pull parallel to the longest side. Yang I have used both pymol and VMD for visualization Tsjerk

[gmx-users] Solvent_box

Hi, I am trying to build a triclinic solvent box around two.pdb using the following commands editconf -bt triclinic -f two.pdb -o three.pdb -d 0.9 -box 20 10 10 genbox -cp three.pdb -cs spc216.gro -o four.pdb -p two.top However the generated pdb file four.pdb shows a cubic solvation box inst

[gmx-users] Re:Error_message

Chris, Thanks for your suggestion. I was downloading the .mdp file in a windows machine and then moving it to the cluster. I moved using the binary format instead of the ASCII and it worked. probably it was inserting some carriage return or other charecters. Thanks once again Prasenjit Kumar Muk

[gmx-users] Error_message

Dr. Spoel, Thanks for your reply. It seems that the program raises 4 exceptions while writing a statusfile in regards to 4 variables (integrator,ns-type, optimize_fft, constraints) in the .mdp file. In all cases one of the possible options for each variable is given in the input .mdp file.Howeve

[gmx-users] Error_message

Hi, I am trying to generate a .tpr file.I am getting the following error message (below). Fatal error: There were 4 error(s) processing your input I could not understand what the error(s) were since nothing else was given.Is there some place where the details of the error will be listed so tha

[gmx-users] Error_message

Hi, I am trying to generate a .tpr file for my ligand and I am getting the follwing error message.I would be greatful if somebody could look into it and tell me what the errors are.Thanks [EMAIL PROTECTED]:~/gromacs/drugenz2/junk> grompp -f em.mdp -c trp_b4ion.pdb -p trp.top -o trp_b4ion.tpr -n

[gmx-users] charge

Hi, I wish to simulate a ligand-protein system..I have used the prodrg server to create the .itp file for my ligand. I have done gaussian charge calculation for my ligand using the chelpg method. how should i incorporate the gaussian charges into my .itp file. should i copy the charges for heavy

[gmx-users] Re: Ligand_charges

Dr Spoel, Thanks for your suggestions. Actually i would be using the GROMOS96 force field(option 0 in pdb2gmx GROMOS96 43a1).I am new to the GROMACS package.I wish to simulate a ligand-protein system and had been using the drug-enzyme tutorial available for this purpose. In the tutorial they use

[gmx-users] Ligand_charges

Hi, I am a new user of GROMCAS.I would like to estimate the partial charges of my ligand using the ChelpG option of the gaussian program. Could you kindly guide me as to how i should carry out this calculation. If there are any online tutorials one this could you kindly direct me to it. Any oth

[gmx-users] Prot_prep_query

Hi, Thanks for your suggestions. I was using the 0 option gromos FF in pdb2gmx. As you said the behavior is strange. However i found a fix. I was using a 2 step procedure 1) strip hydrogen > output pdb 2) input pdb > write output pdb with -inter flag instead i used 1) strip hydrogen > outpu

[gmx-users] Prot_prep_query

come the integration problem (installing > CVS) > (David van der Spoel) >3. Re: question about the total-energy of energy > minimization > (Mark Abraham) >4. Hi all (ann rose) >5. Re: overcome the integration problem (installing > CVS) (Berk He

[gmx-users] Prot_prep_problem

Hello gromacs users, I am facing a particular problem in the preparation of my protein.I have a NMR derived structure with hydrogens. To prepare my protein i thought of a two step procedure 1)stripping the protein of the hydrogens using -ignh and saving pdb output 2)submitting the pdb output fi

[gmx-users] Prot_prep_problem

Hello group users, I am trying to prepare a protein using the pdb2gmx module of gromacs.I have stripped the hydrogens using a different program and using a pdb file as the input.I am getting the following error message. Please help me with your suggestions on this. Thank you kindly. Select the