Hi,
The command for ambpdb should look like this:
ambpdb -p filename.parmtop < filename.ncrst > filename.pdb
Cheers,
Satyajit
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________________________________
From: Siavoush Dastmalchi via AMBER <amber.ambermd.org>
Sent: Saturday, March 11, 2023 2:30:29 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] ambpdb -c flag is unknown
Dear List,
I am getting a weird error for ambpdb. I am using it like this:
ambpdb -p .prmtop -c .ncrst > .pdb
What I get is this message:
unknown flag: -c
I looked at the usage of ambpdb and couldn't see -c flag, but it looks like it is a flag to indicate coordinate file in .rst7 or .ncrst format.
Am I doing something wrong? I think I have used ambpdb before the way I have shown above. After all, how I should tell ambpdb where to look for the coordinates?
Cheers,
Siavoush
pc: help for ambpdb:
Usage:
ambpdb [OPTION]... < restrt > out.pdb
Options:
-p PRMTOP Define PRMTOP filename (default:"prmtop").
-tit TITLE Write a REMARK record containing TITLE.
(default: use prmtop title)
-aatm Left-justified Amber atom names.
-bres Brookhaven Residue names (HIE->HIS, etc.).
-ctr Center molecule on (0,0,0).
-noter Do not write TER records.
-ext Use PRMTOP extended PDB info, if present.
-ene FLOAT Define H-bond energy cutoff for FIRST.
-bin The coordinate file is in binary form.
-offset INT Add offset to residue numbers.
Options for alternate output format (give only one of these):
-pqr PQR (MEAD) format with charges and radii.
-sas PQR with 1.4 added to atom radii.
-mol2 TRIPOS MOL2 format.
-bnd list bonds from the PRMTOP.
-atm Mike Connolly surface/volume format.
-first Add REMARKs for input to FIRST.
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Received on Sat Mar 11 2023 - 01:30:04 PST
