AMBER Archive (2004)

Subject: AMBER: Problem with converting AMBER PREP to MOL2

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Mon Nov 22 2004 - 18:13:39 CST


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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