[AMBER] How to use Amber GAFF force field for methylated DNA

From: MINGREN SHEN <mshen32.wisc.edu>
Date: Fri, 19 May 2017 03:03:15 +0000

Hi, I have been searching the Internet for a while, and I have followed advice from this post ( http://archive.ambermd.org/201006/0461.html ) that I can use PyMoL to add

methyl groups to the PDB file and here is the look of the PDB file:


ATOM 1601 H61 DA 51 -2.765 -4.181 1.967 1.00 0.00 H
ATOM 1602 H2'' DA 51 -9.193 -1.366 -1.465 1.00 0.00 H
ATOM 1603 H5'' DA 51 -9.032 3.743 -1.490 1.00 0.00 H
HETATM 1604 C01 UNK 51 -4.244 -3.293 3.434 0.00 0.00 C
HETATM 1605 H01 UNK 51 -4.860 -2.446 3.356 0.00 0.00 H
HETATM 1606 H02 UNK 51 -4.821 -4.120 3.726 0.00 0.00 H
HETATM 1607 H03 UNK 51 -3.496 -3.117 4.149 0.00 0.00 H
ATOM 1608 P DT 52 -10.794 -0.041 -4.009 1.00 0.00 P
ATOM 1609 C5' DT 52 -8.984 -0.962 -5.666 1.00 0.00 C
ATOM 1610 O5' DT 52 -10.329 -1.050 -5.161 1.00 0.00 O
ATOM 1611 C4' DT 52 -8.394 -2.350 -5.813 1.00 0.00 C
ATOM 1612 O4' DT 52 -7.747 -2.810 -4.592 1.00 0.00 O
ATOM 1613 C3' DT 52 -9.387 -3.463 -6.145 1.00 0.00 C

But I have a question how can I use GAFF for the residues with the name 'UNK' which I am not quite sure how to quickly get what I want.
Since methyl groups is a simple functional group so I think this should already be well studied in GAFF.
And I tried to understand the content of the GAFF tutorial ( http://ambermd.org/tutorials/basic/tutorial4b/ )
According to this tutorial, So I should


  1. set a methyl group into PDB file
  2. using some command like ‘antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2’ to get lib for the 'UNK' residue.
  3. loadoff this lib when using it in the complex of methylated DNA

So is that understanding correct?

But when I do like the tutorial I keep getting the error information like this:

antechamber -i MRS.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2
Running: /home/XX/Software/Amber14/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

---Judge bond type for Residue 1 with ID of 51 and Name of SUS ---

Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
    Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time

---Judge bond type for Residue 2 with ID of 15 and Name of SUS ---

Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
    Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time

Running: /home/XX/Software/Amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 18; net charge: 0

Running: /home/XX/Software/Amber14/bin/sqm -O -i sqm.in -o sqm.out

Running: /home/XX/Software/Amber14/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/XX/Software/Amber14/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/XX/Software/Amber14/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC

And My MRS.pdb is like the following:

USER MOD reduce.3.13.080428 H: found=0, std=0, add=9, rem=0, adj=0
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SUS A 999
HETATM 1604 C01 SUS B 51 -4.244 -3.293 3.434 0.00 0.00 C
HETATM 1605 H01 SUS B 51 -4.860 -2.446 3.356 0.00 0.00 H
HETATM 1606 H02 SUS B 51 -4.821 -4.120 3.726 0.00 0.00 H
HETATM 1607 H03 SUS B 51 -3.496 -3.117 4.149 0.00 0.00 H
HETATM 463 C01 SUS A 15 -4.756 -6.079 3.085 0.00 0.00 C
HETATM 464 H01 SUS A 15 -3.772 -6.433 3.177 0.00 0.00 H
HETATM 465 H03 SUS A 15 -4.812 -5.098 3.454 0.00 0.00 H
HETATM 466 H04 SUS A 15 -5.402 -6.698 3.635 0.00 0.00 H
TER
END

Is there something wrong here?
OR I should adjust the setting to avoid the Warnings?

Thank you!
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 18 2017 - 20:30:02 PDT
Custom Search