normal how to make two pdb in a one file using martinize py scripts

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1 year 2 months ago #7567 by cm
hi,
I have two same pdb and i want to cg the two pdb in a one file.When i have merged the two pdb at a certain distance (using charmm)and coarse grained them by using this
martinize.py -f p1p2.pdb -o system-vaccum.top -x p1p2-CG.pdb -dssp /path/to/dssp -p backbone -ff martini22
the last two residue of one protein missed in p1p2-CG.pdb.
How i will solve the problem.Or is there any other way to convert the two all atom pdb into coarse grained pdb at a certain distance using martinize py scripts.

Thanking you

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1 year 2 months ago #7568 by peterkroon
Hi,

what's the output from martinize?

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1 year 2 months ago #7570 by cm
The last two residue of one pdb are missed in the cg.pdb.All other residue get converted into the cg form.For this reason in the next step I am facing problem because protein. itp file also miss the two residue so there is a coordinator miss match.
Thanking you

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1 year 2 months ago #7574 by cm
anyone have any idea how i can do this.please help me.

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1 year 2 months ago #7575 by peterkroon
Before we can say *anything* sensible we need to see the screen output from martinize. Otherwise we're just guessing and wasting everybody's time.

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1 year 2 months ago #7576 by cm
./martinize.py -f p1p2.pdb -o system-vaccum.top -x p1p2-CG.pdb -dssp /usr/local/bin/dssp -p backbone -ff martini22
INFO MARTINIZE, script version 2.6
INFO If you use this script please cite:
INFO de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO Chain termini will be charged
INFO Residues at chain brakes will not be charged
INFO The martini22 forcefield will be used.
INFO Local elastic bonds will be used for extended regions.
INFO Position restraints will be generated.
WARNING Position restraints are only enabled if -DPOSRES is set in the MDP file
INFO Read input structure from file.
INFO Input structure is a PDB file.
INFO Found 1 chains:
INFO 1: (Protein), 3936 atoms in 258 residues.
INFO Total size of the system: 258 residues.
INFO Writing coarse grained structure.
INFO (Average) Secondary structure has been determined (see head of .itp-file).
INFO Created coarsegrained topology
INFO Written 1 ITP file
INFO Output contains 1 molecules:
INFO 1-> Protein (chain )
INFO Written topology files
INFO Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.


.....this is my screen output.p1p2-CG.pdb missed last two residue
ATOM 558 SC2 ARG 125 -46.592 -18.660 9.922 1.00 6.00 S
ATOM 559 BB GLY 126 -56.074 -20.931 12.049 1.00 0.00 B
ATOM 560 BB CYS 127 -57.946 -21.836 9.913 1.00 0.00 B
ATOM 561 SC1 CYS 127 -57.929 -18.926 8.604 1.00 0.00 S
TER
ENDMDL

also the itp file does not have any information of the last two residue.

thanking you

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1 year 2 months ago #7577 by peterkroon
Hi,

how many atoms and residues are there in p1p2.pdb? Does it work if you try to martinize the proteins separately? Is there a TER record between your proteins?

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1 year 2 months ago - 1 year 2 months ago #7578 by cm
each protein contain 129 residue(i have taken the two same pdb?)there is no ter record between the two pdb.there is a TER record at the end of the combined pdb file.
ATOM 3935 OT1 LEU 129 -61.429 -27.003 6.214 1.00 0.00 PROT
ATOM 3936 OT2 LEU 129 -61.562 -26.115 4.178 1.00 0.00 PROT
TER 3937 LEU 129
END
it work properly when i am taking only one pdb.
Last edit: 1 year 2 months ago by cm.

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1 year 2 months ago #7579 by peterkroon
Hmm.
Could you try putting a TER record between the proteins? If that doesn't work you could first martinize your proteins separately, and merge the pdbs later (by hand)

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1 year 2 months ago #7580 by cm
I did not try that.if I make the coarse grained pdb by martinized py .....Then how I will maintain 30 angstrom distance between them.

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1 year 2 months ago #7581 by peterkroon
Make the PDB with both proteins at 30A, split them again into two pdbs without changing the coordinates, martinize, and combine again.

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