[AMBER] how to choose exclusion policy for GPCR

From: xueqin pang <pangxueqintea.yahoo.com.cn>
Date: Wed, 29 Jul 2009 03:12:33 +0100

Hello everyone,
 I am trying to do molecular dynamics simulation of GPCR with Amber force field FF03 and GAFF running with NAMD. I wondering how to choose exclusion  policy both SCNB and SCEE for the system, or shall I just read the exclusion from Amberprep?
introduction of readexclusions and exclude in NAMD
● readexclusions <Read exclusions from PARM file>
Acceptable Values: yes or no
Default Value: yes
Description: PARM file explicitly gives complete exclusion (including 1-4 exclusions) information. When readexclusions is set to on, NAMD will read all exclusions from PARM file and will not add any more; alternatively, if readexclusions is set to off, NAMD will ignore the exclusions in PARM file and will automatically generate them according to the exclusion policy specified by exclude.
● scnb <VDW 1-4 scaling factor>
Acceptable Values: decimal 1.0
Default Value: 2.0
Description: Same meaning as SCNB in AMBER. Note that in NAMD, 1-4 vdw interactions are DIVIDED by scnb, whereas 1-4 electrostatic interactions are MULTIPLIED by 1-4scaling. So 1-4scaling should be set to the inverse of SCEE value used in AMBER.
● exclude <exclusion policy to use>
Acceptable Values: none, 1-2, 1-3, 1-4, or scaled1-4
Description: This parameter specifies which pairs of bonded atoms should be excluded from nonbonded interactions. With the value of none, no bonded pairs of atoms will be excluded. With the value of 1-2, all atom pairs that are directly connected via a linear bond will be excluded. With the value of 1-3, all 1-2 pairs will be excluded along with all pairs of atoms that are bonded to a common third atom (i.e., if atom A is bonded to atom B and atom B is bonded to atom C, then the atom pair A-C would be excluded). With the value of 1-4, all 1-3 pairs will be excluded along with all pairs connected by a set of two bonds (i.e., if atom A is bonded to atom B, and atom B is bonded to atom C, and atom C is bonded to atom D, then the atom pair A-D would be excluded). With the value of scaled1-4, all 1-3 pairs are excluded and all pairs that match the 1-4 criteria are modified. The electrostatic interactions for such pairs are modified by the constant factor
 defined by 1-4scaling. The
van der Waals interactions are modified by using the special 1-4 parameters defined in the parameter files.
Any suggestions is greatly welcomed.
Thanks so much
Pang Xueqin
Pang Xueqin
State Key Laboratory of Molecular Reaction Dynamics
Dalian Institute of Chemical Physics
Chinese Academy of Sciences.
Tel: +86-411-84379352 Fax: +86-411-84675584

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Received on Wed Aug 19 2009 - 19:36:07 PDT
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