AMBER: ptraj error and min problems

From: Gustavo Pierdominici Sottile <>
Date: Fri, 11 Feb 2005 11:54:23 -0300

Dear Amber users,
                          I have already written due to a problem with
minimization. In that case you told me to see atom number 2110 and it was
and SG atom from a CYX residue that I had forgotten to join with another SG
atom. Now I have done this, but can not arrive to the converge criterion. I
will describe what I did:
>From a structure which does not have energy problems (it has been already
minimized with other program but with the same force field) I practiced a
first minimization and it finished with the message: MAXIMUN NUMBER
With the last structure of this minimization, I did another one and the last
message was: LINMIN FAILURE....
The system is big (30900 atoms) and the convergence criterion small. The
atom number that the .out file denotes is one of a water molecule that
seems not to have any problem.
Perhaps, the structure I have obtained is good enough so as to start the
annealing. Let me know what is your opinion abaout this.
Another topic is that when I use ptraj, it appeared an error message .
ERROR in readParm: ...failed to find BONDS_INC_HYDROGEN
 I used ptraj with a .top file that is in amber7/test/val.... and it is OK.
But I can not see the difference between this file and my file.
I send both min.out files. The outputs of both minimizations are: min.out
and min1.out, corresponding to the first and the second output of what I
explained above.
Pd : the .top file that ptraj can not read exceed the maximun size of what I
can send, nevertheless I will see if I can send it
Thanking in advance

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Received on Fri Feb 11 2005 - 15:53:00 PST
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