<DIV>
<DIV>Dear Anton and Gmx-users,</DIV>
<DIV> </DIV>
<DIV>If without bonds, I think the top file (as shown in urea.top - manual page 100) will like this:</DIV>
<DIV>[moleculetype]</DIV>
<DIV>;name nrexcl</DIV>
<DIV>Urea 3</DIV>
<DIV> </DIV>
<DIV>[atom]</DIV>
<DIV>;nr type</DIV>
<DIV>1 C</DIV>
<DIV>2 O</DIV>
<DIV>3 NT</DIV>
<DIV>4 H</DIV>
<DIV>..</DIV>
<DIV> </DIV>
<DIV>[bonds] ; no need to input</DIV>
<DIV> </DIV>
<DIV>[pairs]</DIV>
<DIV>;ai aj funct b0 kb</DIV>
<DIV> 3 4 1 1.0e-01 3.74468e+05</DIV>
<DIV> 3 5 1 1.0e-01 3.74468e+05</DIV>
<DIV> ...</DIV>
<DIV> </DIV>
<DIV>[angles] ; no need to input</DIV>
<DIV> </DIV>
<DIV>[dihedrals]; no need to input</DIV>
<DIV> </DIV>
<DIV>[position_restraints}</DIV>
<DIV>1 1 1000 1000 10000</DIV>
<DIV>...</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>;include SPC water topology</DIV>
<DIV>#include "spc.itp"</DIV>
<DIV> </DIV>
<DIV>[system]</DIV>
<DIV>Urea in water</DIV>
<DIV> </DIV>
<DIV>[molecules]</DIV>
<DIV>Urea 1</DIV>
<DIV>Sol 1000</DIV>
<DIV> </DIV>
<DIV>Appreciate if you could correct it if any mistakes.</DIV>
<DIV>Besides, how could we select ' without bonds' when we do pdb2gmx or by modifying </DIV>
<DIV>.pdb file ?</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Thanks in advance.</DIV>
<DIV> </DIV>
<DIV>Albert</DIV>
<DIV><BR><BR><B><I>Anton Feenstra <feenstra@chem.vu.nl></I></B> wrote:</DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid; WIDTH: 100%">Victor Kowalenko wrote:<BR>> Hi Anton,<BR>> <BR>> I am sending you this e-mail to confirm that the following is all<BR>> I need to get our atomic modelling working in GROMACS as I am not entirely<BR>> sure that this will work.<BR>> <BR>> First, I need to write a script file that will create *.top file from the<BR>> pdb files. I should mention the format of our pdb files just in case their<BR>> format is unsuitable for GROMACS. They basically go like this:<BR><BR>Whether you need a script depends if you want bonds, without bonds the<BR>.top will be rather trivial and can be written by hand.<BR><BR>> HETATM <PARTICLE No.><TYPE><TYPE><PARTICLE No.>x y z 0.00 0.00 <TYPE><BR>> e.g.<BR>> HETATM 1 Al Al 1 0 0 0 0.00 0.00 Al<BR>> HETATM 2 Cu Cu 2 0 0 1 0.00 0.00 Cu<BR>> etc.<BR>> <BR>> I think the zeros correspond to velocities or some other
units, but they<BR>> are irrelevant for the time being. It is x, y and z coordinates that are <BR>> important. I would like to know if this format is suitable for GROMACS or<BR>> whether I need to write a script file that extracts only the coordinates.<BR>> The files will have to be altered anyway as the coordinate positions are<BR>> in Angstroms while there is a preference for nm in GROMACS.<BR><BR>Close, but not quite there... This looks like the general .pdb format anyway.<BR>The zeroes should be occupancy and B-factor. Irrelevant for us. The units in<BR>Gromacs files are nm, but .pdb is not a Gromacs file format and the official<BR>PDB file format description insists on angstroms. So, in .pdb you must use<BR>Angtroms, and in .gro nm. It looks like Gromacs will read your files just fine.<BR><BR>> As far as the topology file is concerned, it appears to me that if I elect <BR>> only to do atom interactions I only need to create a script file that<BR>>
creates a topology file with only 2 main parts to it: [atomtypes] and<BR>> [atoms]. That is, it should look like:<BR>> <BR>> [atomtypes]<BR>> ; specify the various types of atoms in the simulation<BR>> ; atom atomic mass charge epsilon sigma<BR>> Al 26.98 0 LJ_energy in kJ/mol LJ_radius in nm<BR>> Cu 63 0 LJ_energy_2 in kJ/mol LJ_radius_2 in nm<BR>> [atoms]<BR>> ; nr atom type<BR>> 1 Al<BR>> 2 Cu<BR>> 3 Al<BR>> etc.<BR>> <BR>> where the numbers in the [atoms] correspond to the numbers in the pdb<BR>> files so that GROMACS can get the particle coordinates. <BR>> <BR>> I think this is what you are saying below and if this is correct, then<BR>> I see no problem in writing a little script file to read the pdb file<BR>> a structure file. Please inform me as to whether this is correct or<BR>> whether I have missed something. My aim is to create a general script<BR>> file that will variable numbers of particles in the pdb
files and place<BR>> them in this format. If the pdb format is no good, then I could create a<BR>> new pdb file with the proper format. <BR>> <BR>> Cheers,<BR>> Victor.<BR><BR>Sounds good. You did not include all the obligatory sections above in<BR>your 'example' .top, check the manual for the complete description of<BR>the .top file format.<BR><BR><BR>-- <BR>Groetjes,<BR><BR>Anton<BR>_____________ _______________________________________________________<BR>| | |<BR>| _ _ ___,| K. Anton Feenstra |<BR>| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |<BR>|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |<BR>| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |<BR>| | Feenstra@chem.vu.nl - www.chem.vu.nl/~feenstra/ |<BR>| | "If You See Me Getting High, Knock Me Down" |<BR>| | (Red Hot Chili Peppers)
|<BR>|_____________|_______________________________________________________|<BR><BR><BR>_______________________________________________<BR>gmx-users mailing list<BR>gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.</BLOCKQUOTE></DIV><p><hr SIZE=1>
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