Hi,
I guess you must go ahead and check if you are able to reproduce any experimental phenomenon, for example reproducing binding energy.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Vijay Achari [mailto:glycoamber.gmail.com]
Sent: Thursday, March 16, 2017 5:38 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] Generating topology from Gaussian 09
Dear AMBER experts,
I tried to generate topology file from GAUSSIAN 09 based on tutorial published in online (*
http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-nonstandard/
<
http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-nonstandard/>*)
I have modeled a glycolipid in GaussView.
Then I used options as below to perform the Gaussian calculation.
________________________________________________________
* #Opt B3LYP/6-311g* Pop=MK IOp(6/50=1) *
*Glycolipid*
*C*
*C*
*C*
*O*
*O*
*H*
*H*
*.*
*.*
*.*
*antechamber-ini.esp*
*antechamber.esp *
*__________________________________________________________*
Finally, I used *antechamber* command to generate a PREPIN file.
The command I used is:
*antechamber -i antechamber.esp -fi gesp -o glycolipid.prepin -fo prepi -c resp s 2 -rn DDG at amber -nc 0*
*-i antechamber.esp* (input file)
*-fi gesp* (file format of gaussian)
*-o *glycolipid.prepin (file output)
*-fo prep*i (file format of prepin)
*-c resp* (RESP charge type)
*-s 2* (verbocity)
*-rn* DDG
*-at *amber
*-nc 0* (net charge is zero)
*My question is about the reliability of this method to generate the topology file*. When I check unit in xleap, it says there is no error. I can load the molecule in xleap with no error.
*Can anyone give some comment to clear my doubt?*
Appreciate any help in advance.
Thanks
Vijay
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Received on Thu Mar 16 2017 - 07:30:03 PDT
