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:
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.
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." 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 velocities?
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.
-Justin
Thank you,
Lum
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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