AMBER: phe-phe molecule

From: deepti nayar <>
Date: Mon, 26 Feb 2007 11:31:26 +0530


i have generated the structure for phe-phe using sybyl software. i
generated the prepi file for it with the help of antechamber. but when
i check my protein in xleap it gives many errors regarding non bonded
atoms and angles. now if i generate a frcmod file and manipulate the
parameters there, i am not able to do so because the atom name
convention used in sybyl and amber is different. so i am not able to
find out which atom name correspond to which atom? please help me.

what is the atom name convention followed in amber? how do i make the
atom names same in mol2 file and frcmod/prepi file?
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Received on Wed Feb 28 2007 - 06:07:15 PST
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