Dear amber members,
I am having some difficulty converting amber prep format to mol2 format.
My molecule (TAR) is a 16nt-RNA hairpin with the following sequence which is
in accordance with the all_nucleic94.lib.
5'- RG5 RA RG RC RC RC RU RG RG RG RA RG RG RC RU RC3 - 3'
I have determined all partial atomic charges for TAR using leaprc.rna.ff99 in leap
and saved it in prep format as well as parameter (prmtop) and coordinate files.
I have pasted below a part of the prep file for the first two residues of TAR.
0 0 0
leap-generated prep residue
RG5.res
RG5 INT 0
CHANGE NOMIT DU BEG
0.00000
1 DUMM DU M 0.000000 0.000000 0.000000 0.0
2 DUMM DU M 1.000000 0.000000 0.000000 0.0
3 DUMM DU M 1.000000 1.000000 0.000000 0.0
4 H5T HO M 3.219000 -2.780000 -26.055000 0.429500
5 O5' OH M 4.081000 -2.985000 -25.685000 -0.622300
6 C5' CT M 4.782000 -3.773000 -26.651000 0.055800
7 H5'1 H1 E 4.073000 -4.137000 -27.395000 0.067900
8 H5'2 H1 E 5.240000 -4.625000 -26.149000 0.067900
9 C4' CT M 5.869000 -2.965000 -27.352000 0.106500
10 H4' H1 E 6.511000 -3.646000 -27.911000 0.117400
11 O4' OS S 5.256000 -2.049000 -28.267000 -0.354800
12 C1' CT 3 5.927000 -0.778000 -28.251000 0.019100
13 H1' H2 E 6.227000 -0.512000 -29.263000 0.200600
14 C2' CT B 7.148000 -0.958000 -27.352000 0.067000
15 H2'1 H1 E 7.355000 -0.049000 -26.789000 0.097200
16 O2' OH S 8.283000 -1.362000 -28.122000 -0.613900
17 HO'2 HO E 8.171000 -2.293000 -28.328000 0.418600
18 N9 N* B 4.993000 0.240000 -27.733000 0.049200
19 C4 CB B 5.287000 1.567000 -27.526000 0.122200
20 C5 CB B 4.133000 2.138000 -27.045000 0.174400
21 C6 C B 4.115000 3.524000 -26.730000 0.477000
22 O6 O E 3.180000 4.199000 -26.302000 -0.559700
23 N1 NA B 5.343000 4.117000 -26.971000 -0.478700
24 H1 H E 5.425000 5.101000 -26.764000 0.342400
25 C2 CA S 6.453000 3.467000 -27.458000 0.765700
26 N2 N2 B 7.550000 4.202000 -27.638000 -0.967200
27 H21 H E 7.518000 5.202000 -27.492000 0.436400
28 H22 H E 8.413000 3.761000 -27.925000 0.436400
29 N7 NB E 3.121000 1.189000 -26.948000 -0.570900
30 N3 NC E 6.482000 2.166000 -27.758000 -0.632300
31 C8 CK S 3.681000 0.088000 -27.366000 0.137400
32 H8 H5 E 3.154000 -0.865000 -27.418000 0.164000
33 C3' CT M 6.698000 -2.082000 -26.435000 0.202200
34 H3' H1 E 6.151000 -1.734000 -25.558000 0.061500
35 O3' OS M 7.865000 -2.825000 -26.076000 -0.524600
LOOP
C2' C3'
C2 N3
C8 N7
IMPROPER
C5 N9 C4 N3
C2 H21 N2 H22
N2 N1 C2 N3
C6 C2 N1 H1
C5 N1 C6 O6
C6 C4 C5 N7
H8 N9 C8 N7
C4 C8 N9 C1'
C3' +M O3' P
DONE
leap-generated prep residue
RA.res
RA INT 0
CHANGE NOMIT DU BEG
0.00000
1 DUMM DU M 0.000000 0.000000 0.000000 0.0
2 DUMM DU M 1.000000 0.000000 0.000000 0.0
3 DUMM DU M 1.000000 1.000000 0.000000 0.0
4 P P M 8.407000 -2.815000 -24.559000 1.166200
5 O1P O2 E 7.241000 -2.754000 -23.651000 -0.776000
6 O2P O2 E 9.400000 -3.903000 -24.414000 -0.776000
7 O5' OS M 9.186000 -1.408000 -24.474000 -0.498900
8 C5' CT M 10.525000 -1.290000 -24.963000 0.055800
9 H5'1 H1 E 10.533000 -1.497000 -26.033000 0.067900
10 H5'2 H1 E 11.155000 -2.020000 -24.455000 0.067900
11 C4' CT M 11.090000 0.106000 -24.722000 0.106500
12 H4' H1 E 12.129000 0.128000 -25.051000 0.117400
13 O4' OS S 10.340000 1.055000 -25.486000 -0.354800
14 C1' CT 3 10.200000 2.295000 -24.773000 0.039400
15 H1' H2 E 10.639000 3.101000 -25.360000 0.200700
16 C2' CT B 10.946000 2.116000 -23.450000 0.067000
17 H2'1 H1 E 10.403000 2.585000 -22.629000 0.097200
18 O2' OH S 12.276000 2.632000 -23.550000 -0.613900
19 HO'2 HO E 12.659000 2.279000 -24.357000 0.418600
20 N9 N* B 8.764000 2.566000 -24.573000 -0.025100
21 C4 CB B 8.200000 3.807000 -24.406000 0.305300
22 C5 CB B 6.860000 3.596000 -24.249000 0.051500
23 C6 CA B 6.064000 4.736000 -24.059000 0.700900
24 N1 NC S 6.676000 5.929000 -24.047000 -0.761500
25 C2 CQ S 7.991000 5.984000 -24.214000 0.587500
26 H2 H5 E 8.424000 6.986000 -24.202000 0.047300
27 N6 N2 B 4.741000 4.695000 -23.895000 -0.901900
28 H61 H E 4.212000 5.555000 -23.840000 0.411500
29 H62 H E 4.268000 3.805000 -23.827000 0.411500
30 N7 NB E 6.563000 2.239000 -24.314000 -0.607300
31 N3 NC E 8.848000 4.992000 -24.400000 -0.699700
32 C8 CK S 7.723000 1.674000 -24.508000 0.200600
33 H8 H5 E 7.852000 0.597000 -24.611000 0.155300
34 C3' CT M 10.972000 0.604000 -23.293000 0.202200
35 H3' H1 E 10.105000 0.208000 -22.766000 0.061500
36 O3' OS M 12.196000 0.273000 -22.631000 -0.524600
LOOP
C2' C3'
C2 N3
C8 N7
IMPROPER
C5 N9 C4 N3
H2 N1 C2 N3
C6 H61 N6 H62
C5 N6 C6 N1
C6 C4 C5 N7
H8 N9 C8 N7
C4 C8 N9 C1'
C3' +M O3' P
DONE
........
.......
......
.....
....
...
.
The prep file does include partial atomic charges which sums up to -15 (for
15 phosphate backbone groups)
Now, I would like to convert the prep file into a mol2 file in such a way that
the partial atomic charges are included.
Thinking that antechamber should be reconfigured for larger molecules
(i.e. 500 Da < Molecular Mass < ~10000 Da), I have modified the define.h file
in $AMBERHOME/src/antechamber to adopt the following form:
(I hope that I have not violated the amber licence aggrement by changing the
define.h file !! If so, please let me know. I won't do that again!)
# define COLORTEXT "YES"
# define REDUCEFACTOR 1
# define PI 3.1415926
# define MAXCHAR 100000
# define MAXATOM 1000
# define MAXBOND 2000
# define MAXRING 1000
# define MAXGAS 500 /*maximum gasiteger parameters*/
/*
For MAXRING, no dynamic memory applied since the actuall number is determined
using a recursive function. However, for small and middle-sized molecules,
it is unlikely that the ring num is larger than 1000
*/
# define MAXCYCLE 100
# define OUTPUTSTEP 10
# define MAXTWIST 10
# define ECSLONG 2
# define COSCUT 120
# define DEGRAD 3.1415926/180
# define VDWIDIST 10
# define ESIDIST 14
# define THETACUT 15
# define CUBE 2.0
# define MAXWILDATOM 20
# define MAXSCHAIN 100
# define MAXCES 20
# define MAXBEED 20
# define MAXATOMTYPE 1000
# define MAXVASTATE 5000
# define PSCUTOFF 7
# define MAX_CES_BOND 2000
and recompiled antechamber in $AMBERHOME/src/antechamber
make clean
make install
After the re-installation, I executed antechamber in two ways as follows
1)antechamber -i tar.prep.in -fi prepi -o tar.mol2 -fo mol2 -at sybyl -c bcc -nc -15 -j 5
I got the following output files
ATOMTYPE.INF
ANTECHAMBER_AC.AC0
ANTECHAMBER_AC.AC
divcon.in
divcon.out
ANTECHAMBER_AM1BCC_PRE.AC
ANTECHAMBER_AM1BCC.AC
but nothing concerning tar.mol2. After checking all the output files,
I noticed that only the first resudue (RG5) of my prep file has been processed
and then antechamber has stopped. Moreover, I see only zeros for coordinates and
charges in the ANTECHAMBER* output files above.
Next, I decided not to include bcc and nc flags and re-run antechamber as
follows (thinking that my prep file already includes charges..):
2) antechamber -i tar.prep.in -fi prepi -o tar.mol2 -fo mol2 -at sybyl -j 5
I only got the first three output files as in section 1. Again the ANTECHAMBER*
output files included only the first residue of the prep file and zeros for the coordinates
and charges.
3) I tried antechamber as in section 1 with -at gaff flag
In addition to the first-five output files in section 1, this time I got a tar.mol2 file
but it was hopeless either. The tar.mol2 file included lots of zeros for the first residue
of the prep file and nothing else beyond that.
4) As in section 2 with -at gaff flag
Except for divcon files, I got all output files in section 1 and a tar.mol2 file
as follows which includes only zeros for the first residue of the prep file but nothing else.
.<TRIPOS>MOLECULE
RG5
32 0 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 H5T 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
2 O5' 0.0000 0.0000 0.0000 os 1 RG5 0.0000
3 C5' 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
4 H5'1 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
5 H5'2 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
6 C4' 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
7 H4' 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
8 O4' 0.0000 0.0000 0.0000 os 1 RG5 0.0000
9 C1' 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
10 H1' 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
11 C2' 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
12 H2'1 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
13 O2' 0.0000 0.0000 0.0000 os 1 RG5 0.0000
14 HO'2 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
15 N9 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
16 C4 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
17 C5 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
18 C6 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
19 O6 0.0000 0.0000 0.0000 os 1 RG5 0.0000
20 N1 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
21 H1 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
22 C2 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
23 N2 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
24 H21 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
25 H22 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
26 N7 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
27 N3 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
28 C8 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
29 H8 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
30 C3' 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
31 H3' 0.0000 0.0000 0.0000 DU 1 RG5 0.0000
32 O3' 0.0000 0.0000 0.0000 os 1 RG5 0.0000
.<TRIPOS>BOND
.<TRIPOS>SUBSTRUCTURE
1 RG5 1 TEMP 0 **** **** 0 ROOT
Perhaps there may be a problem with the numbers that I set in
$AMBERHOME/src/antechamber/define.h
but I have received no failure message about MAXATOM size while running antechamber.
I have not been able to figure out so far why antechamber seems to process only
the first residue of my prep file and stops with lots of zeros.....
Could anyone please let me know how I could convert my prep file into a sybyl mol2
file which includes partial charges?
best regards,
Jenk.
Cenk Andac
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Received on Tue Nov 23 2004 - 00:53:01 PST
