On Thu, Aug 18, 2011 at 3:39 AM, Tsjerk Wassenaar <tsjerkw@gmail.com> wrote:
Hey :)

Here is an all Python solution to load a .gro file, including the box
vectors. It simply converts to PDB format and calls cmd.read_pdbstr...
It supports multimodel files. I'll probably add a mechanism to
identify chains from breaks, as the .gro format does not use chain
identifiers, and may add gzip support. Later I'll also add MARTINI
coarse graining, while I'm at it :)

Do you have a fairly complete Python library for parsing GROMACS topology files? I tend to write ad hoc scripts that add CONECT records to MARTINI models. It's easy to do that for lipid bilayers, but I'd love a more general solution that makes it easy to load proteins correctly.

Cheers,

-Michael
 

Hope it helps,

Tsjerk


###

from pymol import cmd
import math

_pdbline    = "ATOM  %5i  %-3s %3s%2s%4i    %8.3f%8.3f%8.3f%6.2f%6.2f
        %1s  \n"
_pdbBoxLine = "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1           1\n"

d2r = math.pi/180

def cos_angle(a,b):
   p = sum([i*j for i,j in zip(a,b)])
   q = math.sqrt(sum([i*i for i in a])*sum([j*j for j in b]))
   return min(max(-1,p/q),1)

def norm2(a):
   return sum([i*i for i in a])

def norm(a):
   return math.sqrt(norm2(a))

def groBoxRead(a):
   b = [10*float(i) for i in a.split()] + 6*[0] # Padding for rectangular boxes
   return b[0],b[3],b[4],b[5],b[1],b[6],b[7],b[8],b[2]

def groAtom(a):
   #012345678901234567890123456789012345678901234567890
   #    1PRN      N    1   4.168  11.132   5.291
   ## ===> atom name,       res name,       res id,    chain
x,                 y,                 z
   return (a[10:15].strip(),a[5:10].strip(),int(a[:5]),"
",10*float(a[20:28]),10*float(a[28:36]),10*float(a[36:44]))

# Simple GRO iterator
def groFrameIterator(stream):
   while True:
       title = stream.readline()
       natoms = stream.readline().strip()
       if not natoms:
           break
       natoms = int(natoms)
       atoms  = [groAtom(stream.readline())  for i in range(natoms)]
       box    = groBoxRead(stream.readline())
       yield title, atoms, box

def pdbOut(atom,i=1):
   return _pdbline%((i,) + (atom[0][:3],) + (atom[1],) + (atom[3],) +
(atom[2],) + atom[4:] + (1,40) + (atom[0][0],))

def pdbBoxString(box):
   nu = math.sqrt(norm2(box[0:3]))
   nv = math.sqrt(norm2(box[3:6]))
   nw = math.sqrt(norm2(box[6:9]))

   alpha = nv*nw == 0 and 90 or math.acos(cos_angle(box[3:6],box[6:9]))/d2r
   beta  = nu*nw == 0 and 90 or math.acos(cos_angle(box[0:3],box[6:9]))/d2r
   gamma = nu*nv == 0 and 90 or math.acos(cos_angle(box[0:3],box[6:9]))/d2r

   return _pdbBoxLine %
(norm(box[0:3]),norm(box[3:6]),norm(box[6:9]),alpha,beta,gamma)

def gro(filename):
   objname = filename[1+filename.rfind("/"):filename.rfind(".")]
   pdb     = []
   model   = 1
   for title, atoms, box in groFrameIterator(open(filename)):
       pdb.append("MODEL %8d"%model)
       pdb.append(pdbBoxString(box))
       pdb.extend([pdbOut(atom,i) for atom, i in
zip(atoms,range(1,len(atoms)+1))])
       pdb.append("ENDMDL")
       model += 1
   cmd.read_pdbstr("\n".join(pdb),objname)

cmd.extend("gro",gro)

###

On Wed, Aug 17, 2011 at 5:11 AM, Jason Vertrees
<jason.vertrees@schrodinger.com> wrote:
> Hi Michael,
>
> PyMOL knows about gromacs files, but needs to better handle .gro
> files, specifically. Currently you have to export to a PDB to read the
> topology.
>
> Please file this on the open-source tracker
> (https://sourceforge.net/tracker/?group_id=4546) and I'll get to it
> ASAP.
>
> Cheers,
>
> -- Jason
>
> On Mon, Aug 15, 2011 at 8:19 PM, Michael Daily <mdaily.work@gmail.com> wrote:
>> Hi all,
>>
>> Is there a direct way to load a gromacs structure file (.gro) in PyMOL? I
>> know it's simple to convert them to pdb using editconf, but I want to load
>> gro files directly (as you can in vmd) because they permit higher max. atom
>> and residue numbers (100K vs. 10K for pdb) and permit longer residue names
>> (4 chars vs. 3 for vmd).
>>
>> Thanks,
>> Mike
>>
>> --
>> ====================================
>> Michael D. Daily
>> Postdoctoral research associate
>> Pacific Northwest National Lab (PNNL)
>> 509-375-4581
>> (formerly Qiang Cui group, University of Wisconsin-Madison)
>>
>> ------------------------------------------------------------------------------
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>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jason.Vertrees@schrodinger.com
> (o) +1 (603) 374-7120
>
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--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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--
Michael Lerner
Department of Physics and Astronomy
Earlham College - Drawer 111
801 National Road West
Richmond, IN   47374-4095