Re: AMBER: prmtop file format

From: Herbert Georg <>
Date: Fri, 24 Oct 2003 16:51:50 -0200

Ok Yong, I've got it. Now it matched perfectly. With this information,
can I just change the equilibrium values of bond lenghts in the flag
¨%FLAG BOND_EQUIL_VALUE¨ in prmtop file so to get it suitable to my
molecule?? can I change the force constants as well?? What if I split
the types of bonds, for example to diferentiate the bonds in an aromatic
ring to produce a quinone character?
If I cando all of that with no trouble, where can I find parameters for
bond force costants and bond equilibrium values that differentiate
between single and double bonds??


Yong Duan escreveu:

>I think dave is best suited to answer these questions. But he is busy,
>so I take a shot ...
>In sander (and other programs), the "atom" indices in the bonding arrays
>are not the atom numbers. They are the pointers to the 3-D coordinate
>arrays. In other words, it points to the X-coordinate of that atom
>within the array. So, atom one would have an index of 0, atom two would
>have an index of 3, and so on. This dated back to the first version of
>AMBER when 64K bytes of memory was considered "huge" (well, relatively).
>In the new format, because of the backward compatibility concern (to the
>existing code) and because not that many people want to re-write this
>part of the program, the simple solution is to keep it that way. But
>"I6" can not accommodate large systems. A nice thing about the new
>format is that it allows future expansion (because the format
>information is provided). However, on our way, we probably forgot to
>update the manual.
>>-----Original Message-----
>>[] On Behalf Of Herbert Georg
>>Sent: Friday, October 24, 2003 10:38 AM
>>Subject: AMBER: prmtop file format
>>I was taking a look at the prmtop file format description in
>>the amber7 manual
>>and in the amber site but it seems that my prmtop file
>>doesn't match the
>>description. It seems that some new flags were added and the
>>format of the flags
>>has changed. Could someone help me out with this new format?
>>For example, in the flag BONDS CONTAINING HYDROGEN the manual
>>and the site have
>>the following description:
>>FORMAT(12I6) (IBH(i),JBH(i),ICBH(i), i=1,NBONH)
>> IBH : atom involved in bond "i", bond contains hydrogen
>> JBH : atom involved in bond "i", bond contains hydrogen
>> ICBH : index into parameter arrays RK and REQ
>>and my prmtop file has the following for that flag:
>> 0 3 1 6 9 1 18
>> 21 5 18
>> 24 5 18 27 5 30 33
>> 5 30 36
>> 5 30 39 5 42 45 1
>> 48 51 1
>> 57 60 7 63 66 7 69
>> 72 10
>>According to the description above, there is an atom numbered 'zero'.
>>Furthermore, there are atoms numbered above 26 which is the
>>total number of atoms.
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Received on Mon Oct 27 2003 - 07:53:01 PST
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