[gmx-users] [Fwd: hi (fwd)]

Xavier Periole x.periole at chem.rug.nl
Wed Jun 16 13:31:29 CEST 2004

David wrote:

>1)The pdb files which I imported from PDB database has many starting
>headers as ATOM,HETATM,FORMUL etc why exactly they need to have these
>things and on what basis they are using these,suddenly in between they
>shift to one another.In pdb file given in GROMACS tutor for methanol had
>only ATOM and the residue name was also only MO1 but the pdb file for
>methanol had many different residues and different starting headers like
>ATOM,HETATM etc.why is this difference.
The explanation of those abbreviations should be on the web site of the pdb:
They basicaly define which type of "atom" is on the given line.

>2)If at all I want to have my own system like a lipid bilayer membrane with
>Glycerol around and perform energy minimization etc by MD simulation how
>should I proceed,I mean what pdb file should I have,how to combine seperate
>pdb files of DMPC membrane and Glycerol.
You basicaly have to do it by hand. Put some glycerol molecules within a 
bilayer. Erase a DMPC and put a Glycerol (if it has to be in the bilayer).

>3)If at all I have a pdb file and I want to create topology file and
>gromacs file can I create on my own,if I use PDBG server or so .top file is
>created but when I am trying to use it in GROMACS it gives me many errors
>like check the directive bonds etc.What does this mean and how to create a
>topology file,do I need experimental data for that.
You need the coordinates of your system, with the atom type, bond angle 
dihedral and
others define by the force field you use to create the topology file. If 
the atom, bond,
dihedral are not define you have to define your self. There is probably 
some information
of how to do in the manual.

>4)When I am importing pdb files I am getting errors like IGP,CIT etc
>residues are not residue topology data base when I used G43a1 force
>field.So what I did was took the list of atoms from the pdb file for
>residue CIT,IGP etc and try to find the residue name with the same list in
>.rtp entries for all force fields G43a1,G43a2 etc.But I could not find
>these residue names neither I could find the list for any other residue
>name in .rtp entry.In this case what should I do,how to proceed further and
>create .top an .gro files etc.
You have to define the topology of those residues is they are not in the 
force field.
You can olso try the PRODRG server ...

>5)In some cases I am getting error as atoms are missing and .gro file is
>not created.The number of atoms list for a particular residue in .rtp entry
>are more when compared to that in the pdb file hence .gro file is not
>created and .top file is also not created properly.what should I do in this
>case. how to proceed further.
You can try to generate the coordinate of the missing atoms. It could be 
trivial or not.
Programs like PDBviewer can probably help you to do that.

>I earnestly request you to please help me in this regard,I will be very
>very grateful to you.I need help of a knowledgeable person like you.Please
>do not get frustrated seeing such a long mail,please do reply me I will be
>witing for your esteemed reply.
Good luck, the beginning is always hard but it get smouther !!!


   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole

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