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

Francesco Pietra francesco.pietra at accademialucchese.it
Sun Oct 25 18:22:03 CET 2009

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

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).

(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

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 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)
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).

(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,

Protein 1
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


> -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
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list