Fwd: [gmx-users] scripts to generate topology CG

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 25 18:56:03 CET 2009

Francesco Pietra wrote:
> On Fri, Oct 23, 2009 at 5:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> Francesco Pietra wrote:
>>>> grep W solvated.gro | wc -l
>>>> and use that number in the topology?
>>> I forgot to add that the graphic program uses the above grep command,
>> I don't understand this statement.
>>> giving the same number of W as the line command. The number of DCCP is
>>> diminished by those deleted in inserting the protein, but the grompp
>>> command complains that .gro does not matches .top. If no further water
>>> is added graphically, everything works.
>> This is where exact commands (in sequence) really help, or at least a
>> stepwise procedure.  Are you adding a protein into a box that contains
>> DCCP+water, or are you inserting the protein into DCCP, then adding water?
>> What is the exact error that grompp is giving you?  That the number of
>> coordinates don't match? atom names don't match?
> What I did follows. I am using the actual filenames and page numbers
> for my reference.
> (1) getting mod21.cg.pdb from mod21.pdb by using the martini awk script (p. 4).
> (2) getting mod21.itp by using dssp, fasta, seq2itp.pl (p. 4).
> (3) downloading dppc_bilayer.gro, editconf to get dppc_bilayer.pdb (p. 4).
> (4) inserting the pore region of the cg protein into the bilayer in
> the obvious orientation, then removing all dppc superimposed to the
> protein plus an extra margin of 10A, to get mod21.aligned.pdb and
> dppc.aligned.pdb (according to as described for all-atoms in the paper
> I referred to in this thread) (p. 4)
> (5) genbox -cp mod21.aligned.pdb -cs dppc.aligned.pdb -box 11 11 11 -o
> mod21+dccp.box.pdb
> resulted in the protein at a corner of the cubic box. This is probably
> because I was using a homology model, i.e., there was no CRYSTAL
> record. It was nonetheless surprising because the two .pdb files to
> combine had the same box size (p. 5).

Box manipulation can be tricky.  I would recommend doing the alignment with 
editconf, for example, to place the bilayer and protein centers at the center of 
the box, you would issue:

editconf -f mod21.aligned.pdb -o mod21.aligned.center.pdb -c -box 11 -bt cubic

And analogously for the bilayer.  If the center must be shifted relative to the 
box center, you can supply to exact coordinates with editconf -center.

> (6) Cut-and-paste adding mod21.aligned.pdb to dppc.aligned.pdb
> resulted in a correct insertion of the pore region into the bilayer,
> the latter correctly oriented. Filename  dppc+mod21.pdb (p. 6).
> The bilayer originally was made of 128 dppc and 2000 W. After
> insertion of the protein, the system was 1 multimeric protein, 85 dppc
> and 1767 W (taking into account that there are 12 atoms per dppc).
> (7) genbox -cp dppc+mod21.pdb -cs water-1bar.303K.gro -box 11 20 11 -o
> dppc+mod21+W.box.pdb
> resulted in the protein at a corner of the solvating box, which only
> comprised the pore  region inserted into the bilayer. I.e., the large
> non-pore region of the protein was not solvated. On making the box
> bigger and bigger also the non-pore region was solvated but the pore
> region exited the bilayer and entered the water region. Which
> situation could not be accepted (pp. 8-9).

I think genbox is inducing this effect because it is trying to assemble your 
system within the -box you have defined.  I am not aware of any known issues 
with using genbox -box, but as a matter of routine, I always define the box with 
editconf prior to running genbox.  Again, I don't know of anything that is 
broken about genbox, but it would be worthwhile to eliminate this as a potential 

> I was unable to detect whether I was using wrong commands with genbox,
> and therefore I abandoned genbox.
> (8) Starting from dppc+mod21.pdb (from step 6) I tried solvating the
> non-pore region of the protein-dppc ensemble by adding a preformed box
> of water (that is, using the methodology of step 4). Thus,
> dppc+mod21.pd was aligned with a water box of 5400 W, removing all W
> superimposed to the non-pore region of mod21+dppc, plus a margin of
> 10A. The ensemble (filename dppc+mod21+W.gro) opens correctly in VMD
> (or as corresponding .pdb file in CHIMERA), that is, the non-pore
> region is solvated (pp. 11-12).
> In my hands, the .pdb file describing this ensemble did not allow to
> generate a .tpr file. The ensemble was made of
> Protein 1 (multimeric)
> DPPC 85
> W 6008
> which data were used for the .top file. Command
> $ grompp -f minimize.mdp -c dppc+mod21+W.gro -p dppc+mod21+W.top -o minimize.tpr
> resulted in error: number of coordinates in coordinate file
> (dppc+mod21+W.gro 5662) does not match topology (dppc+mod21+W.top,
> 9903) (p. 19).

Can you post the first and last few lines of dppc+mod21+W.gro (i.e., "head 
dppc+mod21+W.gro" and "tail dppc+mod21+W.gro")?


> (9) Starting directly from  dppc+mod21.pdb (from step 6), commad
> $ genbox -cp dppc+mod21.pdb -box 10 17 10 -o dppc+mod21.gro
>                      5662 atoms in 3122 residues
>                      Volume: 1700 nm^3
>                      Density: 99.5996
>                      SOL: 0
> followed by command
> $ grompp -f minimize.mdp -c dppc+mod21.gro -p dppc+mod21.top -o minimize.tpr
> where, for the .top file,
> [molecule]
> Protein 1
> DPPC 85
> W 1767   (derived as indicated at step 6)
> generated correctly the .tpr file (p. 20).
> .......................
> I hope to have illustrated in sufficient details the procedure so as
> my mistakes could be detected.
> thanks for help
> francesco
>> -Justin
>> --
>> ========================================
>> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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