You can use leap.
Command "bondbydistance" can generate connectivity automatically.
Use command "set" to assign atom type.
Ye
-----Original Message-----
From: Zahra Khatti [mailto:khatti_za.yahoo.com]
Sent: Wednesday, December 25, 2013 4:02 PM
To: AMBER.ambermd.org
Subject: [AMBER] input file with leap or antechamber?
Dear amberists
I have nanotube pdb file with 570 atom, since there isn't any atom type for
C in my pdb file, which program should be used for building input ,
antechamber or leap?
This is a part of my pdb file that has one residu (CA).
best regards.
ATOM 1 C C A 1 3.917 0.000 0.000 1.00 0.00 ATOM
2 C C A 1 3.725 1.210 2.132 1.00 0.00 ATOM 3 C
C A 1 3.917 0.000 1.421 1.00 0.00 ATOM 4 C C A
1 3.725 1.210 3.553 1.00 0.00 ATOM 5 C C A 1
3.917 0.000 4.263 1.00 0.00 ATOM 6 C C A 1 3.725
1.210 6.395 1.00 0.00 ATOM 7 C C A 1 3.917 0.000
5.684 1.00 0.00 ATOM 8 C C A 1 3.725 1.210 7.816
1.00 0.00 ATOM 9 C C A 1 3.917 0.000 8.526 1.00
0.00 ATOM 10 C C A 1 3.917 0.000 9.947 1.00 0.00
ATOM 11 C C A 1 3.169 2.302 0.000 1.00 0.00 ATOM
12 C C A 1 2.302 3.169 2.132 1.00 0.00 ATOM 13 C
C A 1 3.169 2.302 1.421 1.00 0.00 ATOM 14 C C A
1 2.302 3.169 3.553 1.00 0.00
Z. Khatti, Ph.D student of Physical Chemistry, Department of Chemistry, Iran
University of Science & Technology,Tehran, Iran
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Received on Wed Dec 25 2013 - 00:30:03 PST
