[AMBER] ERROR atom with mass 1 has type alreadydesignated as non-hydrogen type

From: Abhishek TYAGI <atyagiaa.connect.ust.hk>
Date: Thu, 20 Nov 2014 03:01:08 +0000

Hello,


I am using chamber to convert my psf to amber input prmtop file and crd file. My psf file is readable by chamber but their is a error coming from showing "

 <get_atom_parameters>ERROR atom with mass 1 has type alreadydesignated as non-hydrogen type
 <get_atom_parameters> atom 4585 1.0080000000000000 H1


I have seen searched previous emails and found

http://archive.ambermd.org/201210/0383.html


 But, I am still not able to solve my problem, my parameter file have all the information as required but for hydrogen in TIP3 having some problem to read. My molecule is composed of water box.


 details are as follows:


CHAMBER command:


$AMBERHOME/home/cbme/amber14/bin/chamber -top top_first.inp -top top_all36_na.rtf -param par_all27_first.prm -param par_all36_na.prm -xpsf ionized.psf -crd ionized.pdb -p 3.prmtop -inpcrd 3.inpcrd -nocmap

| *****************************************************
| * CHAMBER: Charmm psf to AMBER prmtop convertor *
| * *
| * v1.5 *
| * *
| * Written by: *
| * Mark J. Williamson *
| * Michael F. Crowley *
| * Ross C. Walker *
| * Jason Deckman *
| * Robin M. Betz *
| * *
| *****************************************************


===========================================================
          PSF input parsing summary
===========================================================

                        Number of PSF flags found: 1

                            Number of atoms found: 120993
                         Number of residues found: 43695

                            Number of bonds found: 83181
                           Number of angles found: 51047
                        Number of dihedrals found: 24429
                        Number of impropers found: 57

                           Number of donors found: 0
                        Number of acceptors found: 0
    Number of explicit nonbonded exclusions found: 0

                           Number of groups found: 1

===========================================================

 <get_atom_parameters>ERROR atom with mass 1 has type alreadydesignated as non-hydrogen type
 <get_atom_parameters> atom 4585 1.0080000000000000 H1
 Cannot continue


Please suggest me how to resolve this error.


regards

Abhi
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Nov 19 2014 - 19:30:02 PST