AMBER Archive (2005)

Subject: AMBER: delphi and surface in MMPBSA

From: Yong Xu (yxu_at_mail.sioc.ac.cn)
Date: Thu Oct 20 2005 - 09:07:17 CDT

Dear Prof. Case

(1)does PB calculation need SA?
when I us "MS 0" option, MMPBSA calculation give out following infomation
================================================
=>> Checking sanity
    Checking GENERAL
    PB calc needs SAS calc by MS
Died at /disk8/yxu/bin/mm_pbsa.pl line 422.
================================================

(2) what is the main difference between Molsurf using in MMPBSA/AMBER and MSMS program
should we use SASA surface in solvation free energy calculation?

there are always different output for those two program using the same probe-radius.
for molecule no100.pdb, MMPBSA give out 78.269 with 1.4 A probe-radius

BUT MSMS give out following infomation, which surface should be taken ?
========
command : msms -if no100.xyzr -probe_radius

MSMS 2.5.5 started on compchem
Copyright M.F. Sanner (1994)
Compilation flags -O3 -mips3 -xansi -DVERBOSE -DTIMING -DFUNCPROTO -fullwarn
INPUT no100.xyzr 9 spheres 0 collision only, radii 1.200 to 2.000
PARAM Probe_radius 1.500 density 1.000
REDUCED SURFACE ...
    RS component 0 identified 8 5 3
    2 free edge(s) found in component 0
    RS component #faces #edges #free_edges #vertices genus
         0 10 15 2 9 0
    Time Reduced Surface real: 0.00 user: 0.00 sys: 0.00
ANALYTICAL SOLVENT EXCLUDED SURFACE...
    Component 0
        Time Surface real: 0.00 user: 0.00 sys: 0.00
        Time Singularities real: 0.00 user: 0.00 sys: 0.00
    SES comp. #fac. #edg. #s_edg. #vert. #s_vert. R_h C_h genus
         0 36 66 0 34 0 0 2 0
ANALYTICAL SURFACE AREA :
    Comp. probe_radius, reent, toric, contact SES SAS
      0 1.500 1.976 24.483 57.351 83.810 213.956
TRIANGULATION...
    Component 0
    component#, vertices, edges, faces, genus, density
        0 98 288 192 0 1.169
        Time Triangulation real: 0.00 user: 0.00 sys: 0.00
NUMERICAL VOLUMES AND AREA
    Comp. probe_radius SES_volume SES_area)
       0 1.50 56.473 77.451
    Total ses_volume: 56.473
MSMS terminated normally
Total Time real: 0.02 user: 0.00 sys: 0.00
=======

        

Best regard!

Yong Xu
yxu_at_mail.sioc.ac.cn
2005-10-20

===========================================================
* Yong Xu
* State Key Lab of Bioorganic & Natural Product Chemistry
* Shanghai Institute of Organic Chemistry
* Chinese Academy of Sciences
           
* 354 Feng Lin Road, Xu Hui District
* Shanghai, 200032, China
        
* Email: yxu_at_mail.sioc.ac.cn
* xuyongch_at_yahoo.com
===========================================================

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