Dear Marko,
Thanks a lot for the additional information...
It looks like you are right & your work should help to correct this new bug.
You could also use R.E.D. at q4md-forcefieldtools.org: I guess this
case is fully handled without any bug ;-)
[I saw you used relative weights for the conformations involved: I
would look carefully at the RRMS value (in the RESP output) in this
case versus the case where all the weights are set to their default
value...]
regards, Francois
> thanks for your reply...so, the problem is not depending on the
> number of atoms at all and maybe it becomes more clear with the
> following explanations...
>
> again to explain the error...
> if a group containing x-times-8 (x=1,2,3,4,5,...,n) atoms, within a
> constrained-group-charge and is putted into a respgen inputfile like
> this:
>
> GROUP 16 1.000
> ATOM 1 N
> ATOM 2 H1
> ATOM 3 H2
> ATOM 4 H3
> ATOM 5 C
> ATOM 6 HA
> ATOM 7 CB
> ATOM 8 HB2
> ATOM 9 HB3
> ATOM 10 CG
> ATOM 11 OD1
> ATOM 12 N2
> ATOM 13 HD21
> ATOM 14 HD22
> ATOM 15 C
> ATOM 16 O
> GROUP 14 0.000
> ATOM 17 N
> ATOM 18 H
> ATOM 19 C
> ATOM 20 HA
> ATOM 21 CB
> ATOM 22 HB2
> ATOM 23 HB3
> ATOM 24 CG
> ATOM 25 OD1
> ATOM 26 N2
> ATOM 27 HD21
> ATOM 28 HD22
> ATOM 29 C
> ATOM 30 O
>
>
> you get as RESP input from respgen something like this:
>
> 16 1.000
> 1 1 1 2 1 3 1 4 1 5 1 6 1
> 7 1 8
> 1 9 1 10 1 11 1 12 1 13 1 14 1
> 15 1 16
>
> 14 0.000
> 1 17 1 18 1 19 1 20 1 21 1 22 1
> 23 1 24
> 1 25 1 26 1 27 1 28 1 29 1 30
> 14 0.000
> 1 31 1 32 1 33 1 34 1 35 1 36 1
> 37 1 38
> 1 39 1 40 1 41 1 42 1 43 1 44
>
> but it should be this:
>
> 16 1.000
> 1 1 1 2 1 3 1 4 1 5 1 6 1
> 7 1 8
> 1 9 1 10 1 11 1 12 1 13 1 14 1
> 15 1 16
> 14 0.000
> 1 17 1 18 1 19 1 20 1 21 1 22 1
> 23 1 24
> 1 25 1 26 1 27 1 28 1 29 1 30
> 14 0.000
> 1 31 1 32 1 33 1 34 1 35 1 36 1
> 37 1 38
> 1 39 1 40 1 41 1 42 1 43 1 44
>
> so, there is this an additional blank-line after a x-times-8 fields entry...
> corresponding code lines:
> in ambertoolsxx/ -> antechamber/ -> respgen.c:
>
> if(count >= 8) {
> count = 0;
> fprintf(fpout, "\n");
> }
> they are identical for ambertools1.5 (lines 367-370) and
> ambertools12 (lines 394-397)..
>
> files are attached...
>
> thanks a lot for your efforts...the bug is reported also to junwei
> wang, even with the corresponding code lines...
> as alternative one can use this peace of bash-code to fix the problem too:
>
> inputResp1="nameOfYourRespInputFile"
> lines=(`awk '/[ ]*[0-9]+[ ]*.[0-9]+\.+[0-9]+/,/$/ { while ($0 !~
> /^$/) { print NR; getline } }' $inputRESP1`)
> firstLine=${lines[0]}
> lastLine=${lines[${#lines[.]}-1]}
> # begin from back, otherwise one screws line numbers for using sed!!!
> for (( j = $lastLine ; j >= $firstLine ; j-- )) do
> for (( k = ${#lines[.]}-1 ; k > 0 ; k-- )) do
> if [[ ${lines[$k]} == $j ]]; then
> echo found entry $k with ${lines[$k]} with j $j
> break
> elif [[ ${lines[$k]} < $j ]]; then
> echo couldn\'t find entry with j $j
> echo sed -ne "$j"p $inputRESP1
> sed -ne "$j"p $inputRESP1
> echo sed -i "$j"d $inputRESP1
> sed -i "$j"d $inputRESP1
> break
> fi
> done
> done
> echo
> echo
>
>
> so, thats all at the moment ;)
> all the best
> Marko
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat May 05 2012 - 01:30:03 PDT
