Dear All,
I have compiled AmberTools 1.4 (with bugfixes 1 to 20)
with the Portland Group compilers, v. 11.3 on a 64-bit
Linux (RHEL4) machine. Although the antechamber/sustiva
test now passed, a test in sleap/pdbent failed.
Run.pdbent1 passed, but Run.pdbent2 generated an empty
mdl_1hpv.mol2 file and the content of pdbent2.out is
[gtkleap]$ source leaprc.ff99SB
[gtkleap]$ set default echo on
[gtkleap]$ hpv = loadpdb 1hpv.pdb
hpv = loadpdb 1hpv.pdb
Error: cannot find molecule 478 in the databse
calling "mdlize_mdb( )"
calling "mdlize_resd_bymdb( )"
[gtkleap]$ savemol2 hpv mdl_1hpv.mol2
savemol2 hpv mdl_1hpv.mol2
Error: cannot find molecule hpv in the databse
calling "mdlize_mdb( )"
calling "mdlize_resd_bymdb( )"
[gtkleap]$ quit
quit
Any idea what the problem is and how I can get it corrected?
I will appreciate any help.
Thank you very much!
Shan-Ho
-----------------------------
Shan-Ho Tsai
University of Georgia, Athens GA
On Fri, 29 Apr 2011, Shan-ho Tsai wrote:
>
> Dear Dr. Case,
> Thank you so much for your response. Of course, you are
> absolutely right, I always forget that PGI 7.2 is very
> old by now. After recompiling with the recent PGI 11.3
> the antechamber/sustiva test ran fine.
>
> I really appreciate your response.
> Thanks again,
> Shan-Ho
>
> -----------------------------
> Shan-Ho Tsai
> University of Georgia, Athens GA
>
> On Fri, 29 Apr 2011, dacase.rci.rutgers.edu wrote:
>
>>>
>>> Last year I installed AmberTools 1.4 (with bugfixes 1 to 8)
>>> with Portland Group compilers (PGI v. 7.2.3)
>>
>> I don't have a solution, but rather a question: why do you want to do this?
>> More explicitly: this is a *very* old version of PGI, and the standard GNU
>> compilers should be fine. Someone on the list may have PGI version 7
>> around, but I suspect that the odds are long.
>>
>> ...dac
>>
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>>
>>
>
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Received on Tue May 03 2011 - 13:30:02 PDT
