AMBER Archive (2009)

Subject: Re: [AMBER] GLYCAM: warnings by writing topology

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Wed Jun 17 2009 - 02:50:46 CDT

Hi Francois,

thank you very much for the fast answer.

Yes, it is sp3 everywhere for all these atoms in leaprc.GLYCAM_06 in
AtomTypes section.
However, CG in leaprc.ff03 is sp2-hybridized. Could it be that when I
read leaprc.GLYCAM_06 as a source, still some inconsistency with ff03
remains, which I use as source before? How can I check this? I tried
also to use leaprc.GLYCAM_06 as the only source but somehow log.file is
not written by default as it was always in case of leaprc.ff03 use, so I
cannot say if I have the same Warnings in that case.

Best regards and thank you,

Sergey

FyD wrote:
> Dear Sergey,
>
>> I'd like to carry out MD simulations with the systems consisting both
>> of proteins and carbohydrates. So I'm trying to use GLYCAM06 in
>> AMBER10. From what I've learnt from the previous posts to the Mailing
>> List, I use both ff03 and GLYCAM06 leaprc files as follows in t/xleap:
>>
>> source leaprc.ff03
>> source leaprc.GLYCAN_06
>>
>> It seems like all the needed files are loaded and I can proceed. When I
>> create the topology and coordinates files with the systems containing
>> saccharides it also looks that they are created properly. However, I
>> have the following warnings in the log.file:
>>
>> ** Warning: No sp2 improper torsion term for CG-H1-CG-OH
>> atoms are: C3 H2 C2 O2
>> ** Warning: No sp2 improper torsion term for CG-H1-CG-CG
>> atoms are: C3 H2 C2 C1
>> ** Warning: No sp2 improper torsion term for CG-OH-CG-CG
>> atoms are: C3 O2 C2 C1
>> ... and so on
>>
>> What wrong I could do to get this or should I ignore these warnings?
>
> Warnings are not errors: Usually, you can proceed... However in your
> case, I do not understand why a sp2 atom is found among the
> CG-H1-CG-OH atom types for instance...
>
> more $AMBERHOME/dat/leap/cmd/leaprc.GLYCAM_06
> [...]
> addAtomTypes{
> { "CG" "C" "sp3" }
> { "H1" "H" "sp3" }
> { "OH" "O" "sp3" }
> }
>
> None of these atoms are sp2 but sp3. right ?
>
> regards, Francois
>
>
>
>
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