[gmx-users] CYS1 or CYS2 not CYSH

Osmany Guirola Cruz osmany.guirola at cigb.edu.cu
Thu Dec 16 16:54:44 CET 2004

David wrote:

>On Thu, 2004-12-16 at 14:30 +0000, Osmany Guirola Cruz wrote:
>> I am doing a peptide simuation that have CYS but by default pdb2gmx put 
>>my CYS as CYSH and i need
>>that CYS deprotonated(and without s-s) i read the rtp files and found 
>>CYS1 CYS2 How can i use this residues. i probe change the pdb file (CYS 
>>--->CYS1) but pdb2gmx says CYSH :-(
>>What can i do?
>How about pdb2gmx -ss
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Does not work :-( , my problem is this i have a peptide C-XXXXXXX-C (not 
ciclic)  but
i dont want CYSH in mi gro file(i want it deprotonated and in the rtp 
files i found CYS1
and CYS2). i probed pdb2gmx -ss and pdb2gmx -ss -inter and does not work 
always pdb2gmx
put CYSH.


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