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 - 05:30:03 PDT
