On 9/30/12 1:06 PM, venkatesh s wrote:
Respected gromacs users
now iam buliding the simulation system
for protein + peptide simulation (manually insert the peptide into the
protein structure file after the TER )
following commands i used here
1. pdb2gmx -f 2KW8.pdb -o lpvtg.gro -water tip3p -ignh -chainsep ter
in topol.top file i manually made change as a Protein_chain_A 2 (previously
it is 1)
[ molecules ]
; Compound #mols
Protein_chain_A 2
This does not sound correct to me. You have a large protein and a small
peptide, correct? These should be different proteins and different
[moleculetype] entries, correct? If this is true, you have two distinct
proteins, not two copies of the same one.
2. editconf -f lpvtg.gro -o lpvtg_newbox.gro -c -d 1.0 -bt dodecahedron
3. genbox -cp lpvtg_newbox.gro -cs spc216.gro -o lpvtg_solv.gro -p topol.top
4. grompp -f ions.mdp -c lpvtg_solv.gro -p topol.top -o lpvtg_ions.tpr
fatal error
number of coordinates in coordinate file (lpvtg_solv.gro, 24393)
does not match topology (topol.top, 26811)
and i read following link
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
manually may want update topol.top file, if yes can you explain?
I think you need to revisit step 1.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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