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Electrostatics / apbs-pdb2pqr

APBS - software for biomolecular electrostatics and solvation
http://www.poissonboltzmann.org/
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missing modified phosphorylated residue in PQR file #521

Closed etillym closed 4 years ago

etillym commented 5 years ago

I am a new user I am using the web interface to produce the PQR AND APBS files, for visualization in VMD. I am visualizing an SH2 domain binding to a phosphorylated tyrosine within a peptide. File is 1LCJ I was able to visualize the electrostatic potential of thee SH2 domain nicely in VMD The peptide is missing the modified phosphorylated tyrosine (designated PTR) residue 204.

It seems that it is missing in the PQR file

PQR file: REMARK 1 PQR file generated by PDB2PQR (Version 2.0.0) REMARK 1 REMARK 1 Command line used to generate this file: REMARK 1 --with-ph=7.0 --ph-calc-method=propka --drop-water --apbs-input --ff=parse --verbose --summary peptide1lcj.pdb peptide1lcj.pqr REMARK 1 REMARK 1 Forcefield Used: PARSE REMARK 1 REMARK 1 pKas calculated by propka and assigned using pH 7.00 REMARK 1 REMARK 5 REMARK 5 WARNING: PDB2PQR was unable to assign charges REMARK 5 to the following atoms (omitted below): REMARK 5 26 N in PTR 204 REMARK 5 27 CA in PTR 204 REMARK 5 28 C in PTR 204 REMARK 5 29 O in PTR 204 REMARK 5 30 CB in PTR 204 REMARK 5 31 CG in PTR 204 REMARK 5 32 CD1 in PTR 204 REMARK 5 33 CD2 in PTR 204 REMARK 5 34 CE1 in PTR 204 REMARK 5 35 CE2 in PTR 204 REMARK 5 36 CZ in PTR 204 REMARK 5 37 OH in PTR 204 REMARK 5 38 P in PTR 204 REMARK 5 39 O1P in PTR 204 REMARK 5 40 O2P in PTR 204 REMARK 5 41 O3P in PTR 204 REMARK 5 This is usually due to the fact that this residue is not REMARK 5 an amino acid or nucleic acid; or, there are no parameters REMARK 5 available for the specific protonation state of this REMARK 5 residue in the selected forcefield. REMARK 5 REMARK 6 Total charge on this protein: -3.0000 e REMARK 6

What can I do to create a PQR file for the small peptide that contains the missing phosphorylated residue?

sobolevnrm commented 5 years ago

Hello,

This error typically means that the force field you’ve chosen does not have parameters for your residue. You need to supply those parameters yourself of chose a force field that supports your residue. I’ve added @Engel, Dave Wmailto:dave.engel@pnnl.gov , @Brandi-Lozano, Juan Mmailto:juan.brandi-lozano@pnnl.gov , @Offor, Elvismailto:elvis.offor@pnnl.gov , and @Rallo, Robertmailto:robert.rallo@pnnl.gov for help with this problem.

Thank you.

— Nathan Baker Sent from my mobile device

etillym commented 5 years ago

@sobolevnrm thanks for your response. Does one of the provided force field choices in the web resource to generate PQR file recognize phosphorylated residues (PTR = phosphotyrosine)?

sobolevnrm commented 4 years ago

Hello. Unfortunately, we do not currently have parameters for phosphotyrosine. They can be added by following the documentation at https://apbs-pdb2pqr.readthedocs.io/en/latest/pdb2pqr/extending.html.