Date: Sat, 5 Apr 2014 22:39:38 +0800
Dear David A Case and other Amber users,
I ran into a similar problem like the situation in this topic posted by Rohit
<rohitarora10.gmail.com<rohitarora10.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20ATOMIC%20NUMBER%20section%20in%20prmtop%20file%20-%20Sustiva%20example>
>.
My question is described as follow:
In the tutorial http://ambermd.org/tutorials/basic/tutorial4b/ , there's a
pdb file sustiva_new.pdb and I process it using the following command:
antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc
The atoms in the sustiva.mol2 are assigned the correct gaff atom types,but
the problem arises when sustiva.mol2 is loaded into Leap(AmberTools 13).
The atom type of Cl is correct with the gaff atom type cl,but when I edit
atom Cl in xleap using graphic atom editor, the *ELEMENT* property of the
Cl is found to be *C* , not Cl . Also , the prmtop file created using
saveamberparm command shows the same problem as that described by Rohit <
rohitarora10.gmail.com<rohitarora10.gmail.com?Subject=Re%3A%20%5BAMBER%5D%20ATOMIC%20NUMBER%20section%20in%20prmtop%20file%20-%20Sustiva%20example>>
in original topic.
I have seen the reply from David A Case
<case.biomaps.rutgers.edu<case.biomaps.rutgers.edu?Subject=Re%3A%20%5BAMBER%5D%20ATOMIC%20NUMBER%20section%20in%20prmtop%20file%20-%20Sustiva%20example>>
to the problem and I send this email to ask :
1) Is it the error in the specification of ELEMENT property of Cl that
causes the problem in later prmtop file?
2) What's the function of the ELEMENT property in leap and does ELEMENT
property influence the later calculation in sander (if any)?
The attachment is a snapshot of the graphic atom editor in xleap.
I would greatly appreciate your reply.
Many thanks!
renlo ye
sincerely!
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(image/jpeg attachment: sus-leap.jpg)
