Re: [AMBER] ambpdb -c flag is unknown

From: SATYAJIT KHATUA via AMBER <amber.ambermd.org>
Date: Sat, 11 Mar 2023 09:19:46 +0000

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
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