(unknown charset) Re: [AMBER] loadPdbUsingSeq command

From: (unknown charset) Antonija Tomić <Antonija.Tomic.irb.hr>
Date: Tue, 14 Jun 2011 14:47:26 +0200

Yes, I know that this is very generic error message and that is why I
am so confused.

I have look at the parts of pdb file that, when removed, allowed the
command to succed and there is nothing wrong with them (they have
successfully passed tleap).

This is the tleap script that I have been using:

source leaprc.ff03
loadamberparams parm99.dat
loadamberparams gaff.dat
enzSeq = { ILE VAL GLU SER TYR ILE GLY PHE ILE GLU SER TYR ARG ASP PRO
PHE GLY SER ARG GLY GLU PHE GLU GLY PHE VAL ALA VAL VAL ASN LYS ALA
MET SER ALA LYS PHE GLU ARG LEU VAL ALA SER ALA GLU GLN LEU LEU LYS
GLU LEU PRO TRP PRO PRO THR PHE GLU LYS ASP LYS PHE LEU THR PRO ASP
PHE THR SER LEU ASP VAL LEU THR PHE ALA GLY SER GLY ILE PRO ALA GLY
ILE ASN ILE PRO ASN TYR ASP ASP LEU ARG GLN THR GLU GLY PHE LYS ASN
VAL SER LEU GLY ASN VAL LEU ALA VAL ALA TYR ALA THR GLN ARG GLU LYS
LEU THR PHE LEU GLU GLU ASP ASP LYS ASP LEU TYR ILE LEU TRP LYS GLY
PRO SER PHE ASP VAL GLN VAL GLY LEU HID GLU LEU LEU GLY HID GLY SER
GLY LYS LEU PHE VAL GLN ASP GLU LYS GLY ALA PHE ASN PHE ASP GLN GLU
THR VAL ILE ASN PRO GLU THR GLY GLU GLN ILE GLN SER TRP TYR ARG SER
GLY GLU THR TRP ASP SER LYS PHE SER THR ILE ALA SER SER TYR GLU GLU
CYS ARG ALA GLU SER VAL GLY LEU TYR LEU CYS LEU HIE PRO GLN VAL LEU
GLU ILE PHE GLY PHE GLU GLY ALA ASP ALA GLU ASP VAL ILE TYR VAL ASN
TRP LEU ASN MET VAL ARG ALA GLY LEU LEU ALA LEU GLU PHE TYR THR PRO
GLU ALA PHE ASN TRP ARG GLN ALA HIE MET GLN ALA ARG PHE VAL ILE LEU
ARG VAL LEU LEU GLU ALA GLY GLU GLY LEU VAL THR ILE THR PRO THR THR
GLY SER ASP GLY ARG PRO ASP ALA ARG VAL ARG LEU ASP }
x = loadPdbUsingSeq molecule.pdb enzSeq
check x
saveamberparm x molecule.top molecule.crd
savepdb x moleculeA.pdb
quit

Also, I am sending you molecule.pdb file.

I was wondering is there atom number or residue number limitation when
using loadPdbUsingSeq command in tleap?

Antonija




Citiram David A Case <case.biomaps.rutgers.edu>:

> On Tue, Jun 14, 2011, Antonija Tomić wrote:
>>
>> I have tried to use loadPdbUsingSeq command in tleap but I get the
>> following message:
>>
>> Segmentation fault
>
> This is a very generic error message. No one can help very much without
> knowing the exact commands you used, and probably having your input files, in
> order to be able to reproduce the problem.
>
> You can look at the parts of the pdb file that, when removed, allowed the
> command to succeed: is there anything different about the parts that you
> removed?
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



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Received on Tue Jun 14 2011 - 06:00:03 PDT
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