[gmx-users] pdb2gmx: Can I change the margin 10% to a higher value in the specbond.dat ?

2015-05-21 Thread Zhang, Cheng 
Dear GROMACS experts,

I am using pdb2gmx for a protein with 5 disulfind bond


https://copy.com/kPLlSianI4LtohNy


The distance between each Cys SG are: 0.203, 0.204, 0.204, 0.205, 0.167. As a 
result, 10% margin of any value of the reference length in specbond.dat 
cannot cover all of the 5 Cys SG distance.


I understand that a typical disulfide bond should be about 2.05 Å in length. 
However, if I still want to keep them, can I change the 10% margin to a higher 
value (e.g. 15%)?


Thank you very much.


Yours sincerely

Cheng


(Thank you for Justin's reply at 
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097699.html

Would it be possible if I can simply reply to you for the thread instead of 
creating a new one?)
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Re: [gmx-users] pdb2gmx: Can I change the margin 10% to a higher value in the specbond.dat ?

2015-05-21 Thread Tsjerk Wassenaar 
Hi Cheng,

You can add another entry for a disulfide bond with a different length.

Cheers,

Tsjerk

On Thu, May 21, 2015 at 11:31 AM, Zhang, Cheng c.zhang...@ucl.ac.uk wrote:

 Dear GROMACS experts,

 I am using pdb2gmx for a protein with 5 disulfind bond


 https://copy.com/kPLlSianI4LtohNy


 The distance between each Cys SG are: 0.203, 0.204, 0.204, 0.205, 0.167.
 As a result, 10% margin of any value of the reference length in
 specbond.dat cannot cover all of the 5 Cys SG distance.


 I understand that a typical disulfide bond should be about 2.05 Å in
 length. However, if I still want to keep them, can I change the 10% margin
 to a higher value (e.g. 15%)?


 Thank you very much.


 Yours sincerely

 Cheng


 (Thank you for Justin's reply at
 https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097699.html

 Would it be possible if I can simply reply to you for the thread instead
 of creating a new one?)
 --
 Gromacs Users mailing list

 * Please search the archive at
 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

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 * For (un)subscribe requests visit
 https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
 send a mail to gmx-users-requ...@gromacs.org.




-- 
Tsjerk A. Wassenaar, Ph.D.
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