AMBER Archive (2008)

Subject: AMBER: xleap screen output

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Mar 03 2008 - 15:02:54 CST

I am in troubles in preparing files for xleap in Amber 9 (I use graphic leap as
I have to check the structures of non polymeric molecules involved) coming from
programs that are updated as to atom nomenclature. I mean that I have to change
names such as 0C21 1H10 (from updated programs) to C210 H101 for xleap, and
much more.

This time I am not smart enough in coming out. xleap refuses to write prmtop
and inpcrd files for a system of big protein / big ligand / big POPC membrane.
I was able to solve similar problems for a similar system recently, Not now.

Therefore, may I as ask how to output in full (Linux) what comes out in the
screen in order to appreciate what is wrong? I tried adding to the comand

saveamberparam model# xxx.prmtop xxx.inpcrd

the classical unix 2>&1 | tee screen.out, which was not recognized by xleap.

Must add that parameters and coordinates for protein ligand and membrane are OK
on Chimera.

May be some help can be provided from what I can see on the screen from the
above command:

FATAL: Atom .R<E 2700>.A<H 1> does not have a type.
              <NARG 2701>.A<H 27>
              <E 2750>.A<D2H 10>
                         <E2H 9>
                         <E1H 8>
                         <D1H 7>
                         <GH 6>
                         <B3H 5>
                         <B2H 4>
                         <BH 3>
                         <AH 2>
                         <H 1>
               <NPHE 2751>.A<H 23>
               <E 2811>.A<D2H 10>
                         <E2H 9>
                         <E1H 8>
                         <D1H 7>
                         <GH 6>
                         <B3H 5>
                         <B2H 4>
                         <BH 3>
                         <AH 2>
                         <H 1>
               <NARG 2812>.A<H 27>
Failed to generate parameters

Thanks
francesco pietra

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