[gmx-users] Generating a .gro file from .pdb file
Mark.Abraham at anu.edu.au
Mon Sep 28 16:09:11 CEST 2009
Justin A. Lemkul wrote:
> Lum Nforbi wrote:
>> Hello everyone,
>> Thanks to Justin Lemkul and Thomas Schlesier for replying to my
>> question in vol. 65 issues 96 and 98.
>> I am trying to convert a pdb file to a gro file using pdb2gmx -f
>> waters.pdb -o waters.gro and I get the message:
No, that procedure generates a topology file, it is not the correct tool
for a change of coordinate format (which is almost never needed anyway).
As a side effect, it regularizes an input coordinate file which might
have been in one of various formats, and outputs a coordinate file whose
default format happens to be .gro (but could be a range of
possibilities). I wish tutorial writers would not give new people the
wrong impression about the purpose of this step!
>> Select the Force Field:
>> 0: GROMOS96 43a1 force field
>> 1: GROMOS96 43a2 force field (improved alkane dihedrals)
>> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>> 6: [DEPRECATED] Gromacs force field (see manual)
>> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>> 8: Encad all-atom force field, using scaled-down vacuum charges
>> 9: Encad all-atom force field, using full solvent charges
>> I don't want to use any of these force fields. I want to use the
>> charmm27 one. How do I select that? Do I need to modify the code? If
>> so, where do I find it?
> I believe the CHARMM force fields are in the development version of the
> code (which you can get through git - see the website). CHARMM will
> officially be supported in version 4.1, I believe.
If your .../share/gromacs/top directory has a range of ffcharmm27.*
files then you can "add" CHARMM by editing FF.dat by adding a new entry
and updating the number of entries. It is unsupported before 4.1, however.
>> Also, I read in a Spidertoxin tutorial that editconf can be used
>> to convert a .pdb file to a .gro file. I tried this but error message
>> says: "No velocities found."
When? Surely not during your editconf conversion?
>> I know that pdb files generally do not
>> have velocities and these velocities can be generated by setting
>> genvel=yes in the mdp file. How can a .pdb file contain initial
> That's not an error, really. A .pdb file cannot, by virtue of its
> format, contain velocities. You have it right that you need "gen_vel =
> yes" to get started, once you've reached grompp.
Pedantically speaking, a .gro-formatted file with zeroes for the
velocities is also well-formed input for grompp, but you'll likely need
to equilibrate longer to achieve suitable velocities for your desired
ensemble. Using gen_vel = yes is much the better approach.
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