AMBER Archive (2009)

Subject: [AMBER] Unit name with loadMol2 command

From: Nicholas Musolino (musolino_at_MIT.EDU)
Date: Thu Apr 23 2009 - 14:30:30 CDT

Dear Amber mailing list:

I am trying to generate a prmtop file from a MOL2 file using GAFF in
tleap. I have attached a copy of my MOL2 file, and have included it
in the body of this e-mail too.

The problem I am having is that after calling loadMol2, I am having a
problem using check or saveAmberParm because I can't seem to get the
unit right.

My question is, what defines the unit name when loadMol2 is used? (a)
Is it the line after the "@<TRIPOS>MOLECULE" RTI, which is where tleap
must be getting the MOLX designation in this case? (b) Is it the
field 8 of the atom listings, in this case "MOL"? (c) Could it be
from the @<TRIPOS> SUBSTRUCTURE section, which in this case is also
"MOL"? I have tried making all of these consistent, but I still have
the same problem with check.

I have tried "check MOL", "check MOLX", removing the SUBSTRUCTURE
lines from the mol2 file, tried first using "createunit," and then the
add command. But no luck. I have also played around with the MOL2
file, trying to replicate the approach on pages 82-83 of the Amber 8
Users' Manual (http://ambermd.org/doc8/amber8.pdf), making everything
look like the TP example in the user's manual.

Am I missing something here?

Also, please note that the frcmod file generated has no entries in
this case, so I haven't included it with this e-mail.

Thanks in advance for any help anyone is able to provide!

Best regards,
Nicholas Musolino

> > source /home/musolino/src/antechamber-1.27/dat/leap/cmd/leaprc.ff99
> Loading parameters: /home/musolino/src/antechamber-1.27/dat/leap/
> parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading library: /home/musolino/src/antechamber-1.27/dat/leap/lib/
> all_nucleic94.lib
> Loading library: /home/musolino/src/antechamber-1.27/dat/leap/lib/
> all_amino94.lib
> Loading library: /home/musolino/src/antechamber-1.27/dat/leap/lib/
> all_aminoct94.lib
> Loading library: /home/musolino/src/antechamber-1.27/dat/leap/lib/
> all_aminont94.lib
> Loading library: /home/musolino/src/antechamber-1.27/dat/leap/lib/
> ions94.lib
> Loading library: /home/musolino/src/antechamber-1.27/dat/leap/lib/
> solvents.lib
>
> > source /home/musolino/src/antechamber-1.27/dat/leap/cmd/leaprc.ff99
> ----- Source: /home/musolino/src/antechamber-1.27/dat/leap/cmd/
> leaprc.gaff
> ----- Source of /home/musolino/src/antechamber-1.27/dat/leap/cmd/
> leaprc.gaff done
> Log file: ./leap.log
> Loading parameters: /home/musolino/src/antechamber-1.27/dat/leap/
> parm/gaff.dat
> Reading title:
> AMBER General Force Field for organic mol., add. info. at the end
> (June, 2003)
>
> > loadmol2 cand904_lig.mol2
> Loading Mol2 file: ./cand904_lig.mol2
> Reading MOLECULE named MOLX
>
> > loadamberparams cand904_lig.frcmod
> Loading parameters: ./cand904_lig.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
>
> > check MOL
> check: Argument #1 is type String must be of type: [unit molecule
> residue atom]
> usage: check <unit> [parmset]
> > savePdb MOL cand904_lig.pdb
> savePdb: Argument #1 is type String must be of type: [unit]
> usage: savePdb <object> <filename>
> > saveAmberParm MOL cand904_lig.prmtop cand904_lig.inpcrd
> saveAmberParm: Argument #1 is type String must be of type: [unit]
> usage: saveAmberParm <unit> <topologyfile> <coordfile>

> @<TRIPOS>MOLECULE
> MOLX
> 25 24
> SMALL
> bcc
>
>
> @<TRIPOS>ATOM
> 1 Cl1 2.34810 1.03650 1.31850 cl 1 MOL -0.127100
> 2 C1 0.67411 0.98802 0.77720 c3 1 MOL 0.059400
> 3 N1 -0.17489 0.50179 1.87235 n3 1 MOL -0.342900
> 4 H1 0.37542 2.01169 0.51514 hc 1 MOL 0.125000
> 5 H2 -1.12823 0.47979 1.57575 hn 1 MOL 0.162500
> 6 H3 0.10228 -0.42250 2.12916 hn 1 MOL 0.158200
> 7 C2 0.61960 0.13905 -0.50650 c2 1 MOL -0.234300
> 8 C3 -0.50966 -0.09760 -1.17637 c2 1 MOL -0.113700
> 9 H4 1.57671 -0.27163 -0.85176 hc 1 MOL 0.135800
> 10 H5 -1.46663 0.31335 -0.83095 hc 1 MOL 0.135100
> 11 C4 0.27792 -0.30005 -3.53811 c3 1 MOL -0.200300
> 12 C5 -0.56386 -0.94580 -2.46058 c3 1 MOL 0.011600
> 13 C6 -0.10614 -2.35623 -2.16433 c3 1 MOL -0.201400
> 14 H6 0.23016 -0.86300 -4.47959 hc 1 MOL 0.076900
> 15 H7 1.33503 -0.24430 -3.24598 hc 1 MOL 0.079800
> 16 H8 -0.05857 0.72276 -3.74996 hc 1 MOL 0.086900
> 17 H9 -0.71615 -2.81841 -1.37779 hc 1 MOL 0.081100
> 18 H10 0.93846 -2.37943 -1.82635 hc 1 MOL 0.077000
> 19 H11 -0.17461 -2.99805 -3.05280 hc 1 MOL 0.078200
> 20 C7 -2.04370 -0.95403 -2.88674 c2 1 MOL -0.118600
> 21 C8 -2.89382 -0.03747 -2.51837 c1 1 MOL -0.158500
> 22 C9 -3.73872 0.87418 -2.15311 c2 1 MOL -0.176100
> 23 H12 -2.37854 -1.77841 -3.52791 hc 1 MOL 0.141000
> 24 H13 -4.32846 0.78892 -1.24440 hc 1 MOL 0.130900
> 25 H14 -3.90787 1.77607 -2.73484 hc 1 MOL 0.133200
> @<TRIPOS>BOND
> 1 2 3 1
> 2 2 4 1
> 3 3 5 1
> 4 3 6 1
> 5 1 2 1
> 6 7 9 1
> 7 7 8 2
> 8 8 10 1
> 9 2 7 1
> 10 11 12 1
> 11 11 14 1
> 12 11 15 1
> 13 11 16 1
> 14 12 13 1
> 15 13 17 1
> 16 13 18 1
> 17 13 19 1
> 18 8 12 1
> 19 20 23 1
> 20 20 21 2
> 21 21 22 2
> 22 22 25 1
> 23 22 24 1
> 24 12 20 1
>
> @<TRIPOS>SUBSTRUCTURE
> 1 MOL 1 PERM 0 **** **** 0 ROOT

---------------------------------------------------------------------------
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino_at_mit.edu | 617-253-6675 | Room E19-528

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