was there a URL reference for that topology file?
On Thu, Oct 9, 2008 at 8:43 AM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> easy enough. There is an algorithm that just needs to be augmented. If
> there's a definitive way of doing this, I'm all ears.
>
> Bob
>
>
>
> On Thu, Oct 9, 2008 at 4:57 AM, Angel Herráez <[EMAIL PROTECTED]>wrote:
>
>> I have being able to test successfully some MD files from Amber using
>> 11.7.1 It works very well.
>> I will post the example soon --it may well be run across the web, as the 4
>> files sum 1.5MB gzipped, or at least serve as test files for the
>> collection.
>>
>> However, I am havign a little problem that seems related to the Amber
>> reader. This file has a GTP, with P atoms named PA, PB, PG. Jmol is
>> reading the latter two as lead and protactinium, and drawing too many
>> (long) bonds from them.
>> First I thought it would be a text misaligning issue, but after looking at
>> the
>> topology file I see that there are no columns, just 4-character chunks,
>> and
>> atoms as HE, NE, CA are not being misinterpreted (that is, they are
>> correctly read as hydrogen, nitrogen, carbon).
>> Is there a chance to recognize and fix the problem? I can send the file
>> offlist if needed.
>> I think that the file comes from Amber itself, but I need to double check
>> that
>> with the person that did the work, as well as the AMber version if it is
>> meaningful.
>>
>> This is a portion of the file contents:
>> %FORMAT(20a4)
>> HH31CH3 HH32HH33C O N H CA HA CB HB2 HB3 CG HG2 HG3
>> CD HD2 HD3 CE
>> HE2 HE3 NZ HZ1 HZ2 HZ3 C O N H CA HA CB HB2 HB3 OG HG
>> C O N
>> H CH3 HH31HH32HH33HH31CH3 HH32HH33C O N H CA HA CB
>> HB CG2 HG21HG22
>> HG23OG1 HG1 C O N H CH3 HH31HH32HH33HH31CH3
>> HH32HH33C O N H CA
>> HA2 HA3 C O N H CA HA CB HB2 HB3 CG HG2 HG3 CD OE1
>> NE2 HE21HE22C
>> O N H CH3 HH31HH32HH33HH31CH3 HH32HH33C O N H CA
>> HA CB HB2 HB3
>> CG HG2 HG3 CD HD2 HD3 NE HE CZ NH1 HH11HH12NH2
>> HH21HH22C O N H CH3
>> HH31HH32HH33H1 O H2 O3G PG O1G O2G O3B PB O1B O2B O3A
>> PA O1A O2A O5* C5*
>> H5*1H5*2C4* H4* O4* C3* H3* O3* HO*3C2* H2* O2* HO*2C1* H1* N9
>> C8 H8 N7 C5
>> C6 O6 N1 H1 C2 N2 H21 H22 N3 C4 MG O H1 H2 O H1 H2 O
>> H1 H2
>>
>>
>>
>>
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>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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