I am trying to simulate my Protein-ligand complex using AMBER-FF. I tried all 94,96,99SB, GS etc in Gromacs. However, the ligand atoms like OM is not there. So I have added the required atoms in atomtypes.atp and ffnonbonded.itp as referred in Gromacs site. Now grompp is not firing any errors in recognizing atom-types. And EM is successfully completed. However, in Position-restrained steps I am getting errors like too large bond lengths between atoms, charged group moved too far etc. I have simulated these complexes in Gromos53a6-ff. There is no problem. But, in amber, even in OPLS/AA (earlier), I had faced such errors. If anybody has the corrected or higher amber-ff that can run Protein-ligand complex successful, kindly share with me for which I will be grateful.
Dear Bikash
I dont know, how you have converted parameters and included in atomtypes.atp and ffnonbonded.itp files. Also, you have to include bonded parameters in ffbonded.itp.
For Ligand, you have to use Amber-GAFF force-field. There are tools available to convert amber prmtop to gromacs itp. You can separately prepare parameters-topology file for ligand and this file can be merged with protein topology files.
With best regards,
Rajendra
Dear Mr. Rajendra and Dr. Jarmila,
Thank you very much for your reply and suggestion. Amber-GAFF ff is not available in Gromacs tool. How can i generate the ligand topology. I did it using PRODRG2 and appended it to the protein topology. I have never used Amber as I do not have license. Kindly make me understand how to generate the toplogy which can be recognized by AMBER-GS ff in Gromacs.
Thanking You
Sincerely
Bikash
Following tutorial would be helpful to generate parameters for ligands using AMBER-GAFF. Only steps up to creating ligand prmtop and inpcrd files are necessary. These two files can be used as input to ACPYPE.
http://ambermd.org/tutorials/basic/tutorial4b/
If you have access to Gaussian QM package, following tutorial is for derivation of charges by RESP method. Otherwise, you can use R.E.D package, which uses free QM package such as GAMESS.
http://ambermd.org/tutorials/advanced/tutorial1/section1.htm
Dear bikash sahoo ,
Antechamber and other suggested tools belongs to amber tools package.As an answer to your question about amber license I should notice that amber tools is a free software and can be downloaded by following link.For more information just follow the above tutorials.
http://ambermd.org/AmberTools-get.html
Hope it helps.
HHA
Dear Akher,
If you are using the general Pro-ligand tutorial for MD simulation available on web, then be sure that it will work fine only for the gromos ff.
If you want to use Amber ff in gromacs for Pro-lig MD, then you need to generate ligand toplogy that mimics the Amber format in Gromacs.
Follow this link
http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs
Using Acpype, first you can generate the toplogy only for ligand.
acpype -i lig.pdb (check ur charge and define it, else u ll get error)
After u finish acpype command, u ll find a file name lig_GMX.gro and lig_GMX.itp
NOw copy them to ur working folder, update ur toplogy and proceed as per the Gromacs tutorial.
Little tricky. But, I hope u ll make it.
Dear Bikash Ranjon
I have followed what have you mentioned but it give me error
ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2017 AWSdS |
============================================================================
ERROR: no 'antechamber' executable!
ERROR: no 'antechamber' executable... aborting !
==> HINT1: is 'AMBERHOME' or 'ACHOME' environment variable set?
==> HINT2: is 'antechamber' in your $PATH?
What 'which antechamber' in your terminal says?
'alias' doesn't work for ACPYPE.
ACPYPE FAILED: 1
Total time of execution: less than a second
Can you help me about it?
Hi Khan,
It seems you do not have the antechamber executable in your workinf directory. Please check it out. Alternatively you can use the web service at http://www.ccpn.ac.uk/webapps.
Best,
Bikash
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