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

David spoel at xray.bmc.uu.se
Tue Jun 15 21:38:59 CEST 2004

Hi Gerard,
I am Dinesh Pinisetty.I am a beginner in using Gromacs software.I am doing
my Masters program in USA.I do not have much time to know everything
reading the manual,even my professor is new into this area so even he
cannot help me.
I have some very basic questions so I want to know answers from people like
you who are very very good in this area.Please bear with me.I am very sorry
if my questions are silly and I disturb you.

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.

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.

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.

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.

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.

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.

Thanks a lot in advance.............

Yours sincerely,
Dinesh Pinisetty.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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