[gmx-users] Generating a .gro file from .pdb file

Mark Abraham 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 
>> 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.

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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