AMBER Archive (2008)

Subject: AMBER: RESP charges

From: Jena M (jeninhas_at_hotmail.com)
Date: Tue Apr 22 2008 - 07:31:54 CDT

Hi
 
 
I have a ligand bound to a cysteine and I want to derive resp charges for them. I started by building a model system, CH3-S-ligand, where the CH3-S- portion models the CYS aa. Then I submitted this model system to Gaussian in order to obtain the ESP information.
I know how to do the RESP fit for the model system: antechamber -i model.log -fi gout -o model.mol2 -fo mol2 -c resp -s 2. However, what I want is to derive the resp charges for the complete CYS-ligand molecule, using the resp charges (derived from the model system) obtained for the ligand-S-CH2 part and fixing the charges of the rest of the atoms of the CYS with those from the ff99 force field.
I thought to start by generating an antechamber_ac.ac file and hence I created a mol2 file of the complete CYS-ligand molecule and ran the command:
antechamber -fi mol2 -fo ac -i CysLigand.mol2 -o CysLigand.ac -c mul -at amber &
However I obtained the following error:
Cannot successfully assign bond type for this molecule, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase MAXVASTATE in define.h and recompile bondtype.C
 
Here is part of my mol2 file:
 
@<TRIPOS>MOLECULE
generated by VMD
   63 62 1 0 0
SMALL
NO_CHARGES
****
Energy = 0
 
@<TRIPOS>ATOM
      1 N -28.1720 61.0770 10.9360 N 608 CYS 0.000000
      2 CA -27.4200 59.9290 11.4470 CA 608 CYS 0.000000
      3 C -26.1320 60.4310 12.1050 C 608 CYS 0.000000
      4 O -25.2330 60.9580 11.4450 O 608 CYS 0.000000
      5 CB -27.0890 58.9240 10.3360 CB 608 CYS 0.000000
      6 SG -26.7450 57.2030 10.9240 SG 608 CYS 0.000000
      7 HT -27.7950 61.6300 10.1530 HT 608 CYS 0.000000
      8 HA -28.0320 59.4030 12.1800 HA 608 CYS 0.000000
      9 HB1 -26.1990 59.2760 9.8130 HB1 608 CYS 0.000000
     10 HB2 -27.9410 58.8740 9.6580 HB2 608 CYS 0.000000
     11 C20 -42.4710 59.5490 17.4820 C20 1608 PPH 0.000000
     12 C19 -40.1750 59.0240 18.3790 C19 1608 PPH 0.000000
     13 C18 -41.2800 58.6270 17.4250 C18 1608 PPH 0.000000
     14 C17 -41.2340 57.5510 16.5830 C17 1608 PPH 0.000000
 
 
Pehaps this is not the correct way to derive the resp charges for the complete CYS-ligand molecule. I thought that after generating the ac file for the complete CYS-ligand molecule I could generate the resp.in files and fix the resp charges for the ligand and for the backbone atoms of the CYS residue. Could someone please help me?
 
Thanks,
Jena
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