AMBER Archive (2007)

Subject: Re: AMBER: how to combine two molecules

From: Wenyong Tong (wenyong_tong_at_yahoo.com)
Date: Sat Aug 11 2007 - 20:48:48 CDT

Hi, Amber Users,

I can combine my two pdb files now: one is sugar
produced by Leap; another is lipid, and I used
antechamber to get
.prepin and .frcmod files. There is an ether bond
(O-C-O) between one sugar and lipid tail. I used “
bond “ command to connect them.

Although I modify the .frcmod files produced by
antechamber for lipid like the following:
            
# remark goes here
MASS

BOND
OS-c3 386.000 1.425 # Jcc, 7, (1986), 230

ANGLE

OS-c3-c3 67.800 108.7
OS-c3-h1 50.900 106.2 # JCC,7, (1986),230
OS-c3-h1 50.900 106.2
CG-OS-c3 100.00 117.6 # JCC,7, (1986),230

DIHE

IMPROPER

NONBON

I still got the following warning:

Could not find bond parameter for OS-c3
Could not find angle parapeter: OS-c3-h1
                                OS-c3-h1
                                OS-c3-c3
                                CG-OS-c3

I don’t understand why it cannot recognize the
parameter

I give. Anyone can give me some suggestion for this,
and so I can get the .top and .crd file, and then go
for vacation J.

Thanks in advance

Wenyong @Pharmacology, McGill University, Canada

       
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