Dear Amber Community,
With respect to obtain the effective born radii for a specific structure ( using for example imin = 1 or 5 ):
In sander program,
1.
egb.F90 : In subroutine egb_calc_radii ,
if rbornstat == 1 it seems that the effective radii is stored but not printed.
2.
runmd.F90 : Here if rbornstat == 1 the
580 format STATISTICS OF EFFECTIVE BORN RADII OVER ',i7,' STEPS
The statistics over the MD is printed .
3.
force.F90 : Is the subroutine that call the egb_calc_radii
4.
Thus, it seems that we can obtain only average values and only when running MD.
________________________________
De: Carlos Simmerling <carlos.simmerling.stonybrook.edu>
Enviat el: diumenge, 28 de juliol de 2024 21:43
Per a: Jaime Rubio Martinez <jaime.rubio.ub.edu>; AMBER Mailing List <amber.ambermd.org>
Tema: Re: [AMBER] Effective Born Radius
See rbornstat in the manual
On Sun, Jul 28, 2024, 12:43 PM Jaime Rubio Martinez via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
Dear Amber Community,
Given a Protein-ligand geometry, I would like to have the effective Born radius obtained in a GB calculation ( igb=2, for example ). How could I obtain them with SANDER or with PMEMD ?
Thank you in advance
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Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener.
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Received on Sat Aug 03 2024 - 05:00:02 PDT
