Re: [AMBER] tleap command for disulfide bonds: for chain A and Chain B ???

From: Anselm Horn <Anselm.Horn.biochem.uni-erlangen.de>
Date: Wed, 03 Feb 2010 10:17:40 +0100

Hi,

>> On Tue, Feb 02, 2010, Siddharth Rastogi wrote:
>> But when I tried with the Chain B residues, the tleap complains like
>> follows:
>>
>>> bond NF.3.SG NF.51.SG
>> bond: Argument #1 is type String must be of type: [atom]
>> usage: bond <atom1> <atom2> [order]

a very simple way to overcome that problem is running leap twice:

1, generate a structure without any disulfide bonds, but with unique
residue numbers
2, change CYS to CYX and add the disulfide bond commands using the new
residue numbering

All the best,

Anselm

Bioinformatik
Institut für Biochemie
Emil-Fischer-Zentrum
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany


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Received on Wed Feb 03 2010 - 01:30:05 PST
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