Dear Junjian,
> with RED, when perform multiple conformations charge fitting, how to
> change the weights for each conformation?
Sorry I was not in the lab & did not have any Internet access...
Let's start from the version III.4 .
http://q4md-forcefieldtools.org/RED/
- First define the weights your want to use in the MAIN PROGRAM
section (i.e. after line 4190 for instance):
* let's say you have two conformations & a single molecule
# molecule 1; conformation 1
$weight[1][1] = "0.60";
# molecule 1; conformation 2
$weight[1][2] = "0.40";
* if you have two molecules (this could be the same molecule
duplicated to run two different single molecule fit sequentially)
# molecule 1; conformation 1 (let's say you have two conformations)
$weight[1][1] = "0.60";
# molecule 1; conformation 2
$weight[1][2] = "0.40";
# molecule 2; conformation 1
$weight[2][1] = "1.00";
# molecule 2; conformation 2
$weight[2][2] = "1.00";
- then replace:
1) line 2262 by
printf INP1 (" %s project. RESP input generated by R.E.D.\n &cntrl\n
ioutopt=1, iqopt=1, nmol=$nbtot[$NM], ihfree=1, irstrnt=1, qwt= %1.4f
\n &end \n %1.2f\n %s \n%5s%5d Column not used by RESP (Added
by R.E.D. for
information)\n",$CHR_TYP,$qwt,$weight[$NM][1],$TITLE[$NM],$CHR_VAL[$NM],$nbatoms[$NM]);
2) line 2304 by
if ($j < $nbmod[$NM]-1){
printf INP1 ("\n %1.2f\n %s
\n%5s%5d\n",$weight[$NM][1],$TITLE[$NM],$CHR_VAL[$NM],$nbatoms[$NM]);
}
else {
printf INP1 ("\n %1.2f\n %s
\n%5s%5d\n",$weight[$NM][2],$TITLE[$NM],$CHR_VAL[$NM],$nbatoms[$NM]);
}
3) line 2333 by
printf INP2 (" %s project. RESP input generated by R.E.D.\n &cntrl\n
ioutopt=1, iqopt=2, nmol=$nbtot[$NM], ihfree=1, irstrnt=1, qwt= 0.001
\n &end \n %1.2f\n %s \n%5s%5d Column not used by RESP (Added
by R.E.D. for
information)\n",$CHR_TYP,$weight[$NM][1],$TITLE[$NM],$CHR_VAL[$NM],$nbatoms[$NM]);
4) line 2360 by
if ($j < $nbmod[$NM]-1){
printf INP2 ("\n %1.2f\n %s
\n%5s%5d\n",$weight[$NM][1],$TITLE[$NM],$CHR_VAL[$NM],$nbatoms[$NM]);
}
else {
printf INP2 ("\n %1.2f\n %s
\n%5s%5d\n",$weight[$NM][2],$TITLE[$NM],$CHR_VAL[$NM],$nbatoms[$NM]);
}
- If you have intra-molecular charge constraints in your P2N files you
could proceed the way the lines 2391, 2446, 2503 & 2539 (but with INP3
& INP4 instead of INP1 & INP2).
- If you have $n P2N files (i.e. for $n molecules), each single
molecule charge fit will be affected (i.e. in all the 'Mol_$n'
directories) by these modifications, but the multiple molecule charge
fit will not (i.e. in the 'Mol_MM' directory).
If you need more help, do not hesitate to ask; describe what you exactly need.
I hope this helps.
regards, Francois
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Received on Tue May 03 2011 - 02:30:04 PDT
