I am dealing with DNA-drug interaction studies. For the simulation I am using amber 03 force field in GROMACS 4.5.5 . To parametrize the ligand Quercetin I am using antechamber. I am trying to get RESP charges for the optimized structure of the ligand by using the below command,
#P HF/6-31G* opt Pop=MK IOp(6/33=2,6/41=10,6/42=17)
After that I used antechamber,
antechamber -i quer.log -fi gout -o quer.mol2 -fo mol2 -c resp
But I am getting the error as
"Amber8 Module: resp
Unit 10 Error on OPEN: ANTECHAMBER.ESP
Amber8 Module: resp
Unit 3 Error on OPEN: qout
Cannot open charge file QOUT , exit"
Could anyone help me with this?
But If I use -c mul instead of -c resp then I can get the correct output. But I know choosing Mullikan charges may not be the correct option. So I need your kind suggestion to overcome this error.
With regards,
R. Radhika
Maybe you can use RED instead, see the following website:
http://q4md-forcefieldtools.org/RED/
Hope this helps.
At first, I suggest to use ParmBSC0 force-field for the DNA.
Have you checked "quer.log" file, ESP was calculated by Gaussian.
Note (http://ambermd.org/tutorials/advanced/tutorial1/section1.htm):
IOp 6/33=2 makes Gaussian write out the potential points and the potentials - Do not change.
IOp 6/41=10 specifies that 10 concentric layers of points are used for each atom.
IOp 6/42=17 specifies the density points in each layer - 17 gives 2500 points per atom. For larger molecules it may be necessary to reduce this slightly. The maximum number of ESP points that RESP can utilize is 99,999. The value of 17 can be reduced to any integer value.
The input files are generated from the final structure produced during the optimization step. Note that the use of 6/41=10 and 6/42=17 is specific to this project in order to increase the number of grid points that Gaussian produces. For most 'standard' RESP fits these should not be included and just the IOp(6/33=2) is needed.
Hello Dr. Rajendra Kumar,
I have checked quer.log file and the ESP was calculated in the output . But still I couldn't fit the RESP yet. I will check the link which you have sent. Thanks for the reply..
Which Ambertool version you are using? It appears that intermediate output files are not generating. Are you sure that you have permission to write file in the given directory.
If you want to do simulations in Gromacs, you can download and install recent version pf AmberTool, which is freely available.
http://ambermd.org/
http://ambermd.org/AmberTools14-get.html
I think you have to specify a total charge in your command. Like the following command -nc means netcharge. See if it works like this way...
antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c resp -s 2 -nc 1
Dear Symon,
The RESP charges have to be handled in a different way. -nc is for denoting the total charge of the system. That is where i am lacking..
Dear Dr. Rajendra Kumar,
Thanks for the help. I have created the topological file with the resp charges with your guidance.
With regards,
R. Radhika
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