Re: [gmx-users] on PDB2gmx

Hi Peter,   I mean if before we input the pdb file to the pdb2gmx, we predetermine the protonation state of HIS, then the corrected PDB file will decide the protonation state of HIS, rather pdb2gmx will assign the protonation state, as for the coordinates of the protonation H will exist in the c

[gmx-users] Protein charge

Hi all, I've a simple question: Is there a tool with which you can charge a protein after a certain pH-value? Best regards, grita -- View this message in context: http://gromacs.5086.n6.nabble.com/Protein-charge-tp4704321p4704321.html Sent from the GROMACS Users Forum mailing list archive at N

[gmx-users] on the .rtp file

Dear All, Suppose in my PDB file for pdb2gmx I will include HISD, HISE, etc, will you please tell me how to construct or find the the .rtp file? And the command to use the .rtp file in the pdb2gmx?   Cheers,   Acoot  -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

[gmx-users] MPI installation

Hi, I am trying to enable mpi fro mdrun in an already installed gromacs-4.5.5. But while executing the command make mdrun , I am getting the following errorn:- mv -f .deps/xlate.Tpo .deps/xlate.Plo /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 -fomit-frame-pointer -finline-functions -Wal

Re: [gmx-users] Is the PME domain decomposition flexible in some hidden way?

Thank you very much for the help. I read the part of the manual you referred to, it is now clear how to choose the decomposition. Cheers Paolo On 3 April 2012 17:16, Mark Abraham wrote: > On 3/04/2012 11:58 PM, Paolo Franz wrote: > >> Hello! >> I am wondering if the domain decomposition chosen b

Re: [gmx-users] how pdb2gmx calculate the total charge of a protein

Charge assignment is dependent on forcefield. If the forcefield results in integral charges for polar residues then that's what you get. (Most classical FFs do.) I could be wrong but I don't think gromacs supports polarizable forcefields. On 2012-04-07 02:21:42AM -0700, Acoot Brett wrote: > Than

Re: [gmx-users] how pdb2gmx calculate the total charge of a protein

Thanks Francesco.   But at any pH value (different protonation state), the H cannot be regarded as fully associated or dissociated. Thus can we further consider whether the total charge calculated by pdb2gmx is really the net charge of the system or not. I regard the net total charge, regardless

Re: [gmx-users] how pdb2gmx calculate the total charge of a protein

Dear Acoot, the error, I guess, is you assumed the histidines are positive while I think they are neutral. Since the His protonation state is hard to identify at ph7, Hystidines are usually neutral. Francesco Il 07/04/2012 09:42, Acoot Brett ha scritto: Dear All, I have a protein, the cha

[gmx-users] how pdb2gmx calculate the total charge of a protein

 Dear All,   I have a protein, the charged residue numbers in the protein is as following ARG  11 ASP  19 glu  25 his  8 lys  24   asp+glu=   44 arg+his+lys=43   However the total charge of the protein given by pdb2gmx is -9.   Will you please introduce to me how pdb2gmx calculate the total charge