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
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Received on Fri Dec 19 2008 - 18:46:57 PST
