AMBER Archive (2008)

Subject: AMBER: idecomp=2 & RRES/LRES group specification

From: In Hee Park (ipark_at_chemistry.ohio-state.edu)
Date: Fri Dec 19 2008 - 19:19:43 CST

Amber users,

I wanted to create a sander input with a group specification in case of
idecomp = 2, like a same way of decomposed MMGBSA, but wanted to add
single residue fragment to the receptor and ligand parts.

I trid to find more information by referring to
"$AMBER/src/sander/rgroup.f" and tried to follow its instruction,
  ///////////
  RES CARD LISTS RESIDUE GROUPS IGRP(I) TO JGRP(I) ----

  IF 1ST VALUE IS NEGATIVE, THEN EVERY RESIDUE FROM IGRP(I)
  TO JGRP(I) IS CONSIDERED A SEPARATE GROUP
  IF 2ND VALUE = 0, THEN SUBGROUP CONSISTS OF 1 RESIDUE
  ATOM CARD READS IN GROUPS OF ATOMS
  IF 2ND ATOM IN EACH PAIR = 0 , THEN SUBGROUP CONSISTS OF
  1 ATOM RES AND ATOM CARDS MAY BE READ IN ANY ORDER
  END INPUT WITH AN "END " CARD

  ZERO NGRP BEFORE CALLING THIS ROUTINE
  ROUTINE WILL RETURN WITH THE NUMBER OF THE LAST GROUP READ
  ///////////
but still got the same ****PROBLEMS WITH GROUPRES problem***.

Does anyone have more information how to do group specification using
"RRES/LLRES" in order them to correctly read in
 "Number of atoms in this group = "? (which is zero now below.)

Following is the sander input group specification part and
corresponding sander output.

=============
sander intput
=============
....
 &end
Residues considered as REC
RRES 1 113 227 227
END
Residues considered as LIG
LRES 114 226 229 229 228 228
END
Residues to print
RES 1 113 227 227 114 226 229 229 228 228
END
END

=============
sander output
=============
    LOADING THE DECOMP ATOMS AS GROUPS

    ----- READING GROUP 1; TITLE:
 Residues considered as REC
      ***PROBLEMS WITH GROUPRRES 1 113 227 227 0 0 0
0 0 0 0 0 0 0*******

      Number of atoms in this group = 0
    ----- READING GROUP 2; TITLE:
 Residues considered as LIG
      ***PROBLEMS WITH GROUPLRES 114 226 229 229 228 228 0
0 0 0 0 0 0 0*******

      Number of atoms in this group = 0
    ----- READING GROUP 3; TITLE:
 Residues to print
 GRP 3 RES 1 TO 113
 GRP 3 RES 227 TO 227
 GRP 3 RES 114 TO 226
 GRP 3 RES 229 TO 229
 GRP 3 RES 228 TO 228
      Number of atoms in this group = 3640

Thank you for your help in advance.

_____________
In-Hee Park
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu