Hi,
Please post your entire cpptraj input. Also, what version of cpptraj are
you using?
-Dan
On Mon, Mar 27, 2017 at 10:52 AM Andreas Tosstorff <
andreas.tosstorff.cup.uni-muenchen.de> wrote:
Thanks for the link Elvis, however I do not want the discussion to lead
away from the main issue here. Does anybody else have suggestions on why
cpptraj is not calculating a single SASA value for my residue 1?
On 03/27/2017 03:24 PM, Elvis Martis wrote:
> Hi,
> Here is an old post regarding this
http://archive.ambermd.org/201603/0076.html.
> I guess nothing much you can do about this.
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry)
> at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in
> Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Andreas Tosstorff [mailto:andreas.tosstorff.cup.uni-muenchen.de]
> Sent: Monday, March 27, 2017 6:20 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] surf cpptraj non-standard residue
>
> Thank you for your reply! I am not sure if this is the cause of the
problem, since the output looks the same for residues 2 to 10 and the
message is actually referring to Chloride Ions which are not part of the
residue. Do you know how to load the parameters for Cl- ?
>
>
> On 03/27/2017 02:38 PM, Elvis Martis wrote:
>> It seems the LCPO method does not have the parameters for those atoms
hence it assigns carbon SA parameters to compute the SASA.
>>
>>
>> Best Regards
>>
>>
>>
>> Elvis Martis
>> Ph.D. Student (Computational Chemistry)
>> at Bombay College of Pharmacy
>>
>>
>> A Kalina, Santacruz [E], Mumbai 400098, INDIA W www.elvismartis.in
>> Skype. adrian_elvis12
>>
>>
>>
>>
>> -----Original Message-----
>> From: Andreas Tosstorff [mailto:andreas.tosstorff.cup.uni-muenchen.de]
>> Sent: Monday, March 27, 2017 5:59 PM
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: [AMBER] surf cpptraj non-standard residue
>>
>> Hi all,
>>
>>
>> I stumbled across a problem analysing the trajectory of a peptide
containing non-standard amino acids using the surf function in cpptraj.
>> The non-standard residue is the first in the sequence (R1).
>>
>> These are the commands I used in cpptraj:
>>
>> parm DIM_solv.parm7
>>
>> trajin DIM_solv_prod.crd
>>
>> surf R1 :1 out sasa1.dat
>>
>> ...
>>
>> surf R10 :10 out sasa10.dat
>>
>> run
>>
>>
>> The cpptraj output looks like this:
>>
>> ACTION SETUP FOR PARM 'DIM_solv.parm7' (10 actions):
>> 0: [surf R1 :1 out sasa1.dat]
>> LCPO surface area will be calculated for 14 atoms.
>> 14 solute atoms.
>> Warning: Using carbon SA parms for unknown atom 175 type Cl-
>> Warning: Using carbon SA parms for unknown atom 350 type Cl-
>> Warning: Using carbon SA parms for unknown atom 352 type Cl-
>> Warning: Using carbon SA parms for unknown atom 353 type Cl-
>>
>> ...
>>
>>
>>
>> For R2 to R10 I the files sasa*.dat look fine, I receive one value per
frame. However for sasa1.dat I get 10 values per frame:
>>
>> #Frame R
>> 1 177.0622 140.8356 164.5719 57.5352 163.3728
>> 122.6951136.7847 169.207108.0297 148.5364
>>
>> ...
>>
>> This is what desc R1 gives me in tleap:
>>
>>
>> RESIDUE name: PCA
>> RESIDUE sequence number: 1
>> RESIDUE PDB sequence number: 1
>> Type: undefined
>> Connection atoms:
>> Connect atom 1: A<C5 7>
>> Improper torsions:
>> Contents:
>> A<H6 15>
>> A<H5 14>
>> A<H4 13>
>> A<H3 12>
>> A<H2 11>
>> A<H1 10>
>> A<O2 8>
>> A<C5 7>
>> A<O1 6>
>> A<C4 5>
>> A<C3 4>
>> A<C2 3>
>> A<C1 2>
>> A<N1 1>
>> >
>>
>> How can I get cpptraj to print the SASA for the entire residue? Is there
something wrong with the parameter file?
>> Thanks in advance for your help!
>>
>> Best,
>> Andy
>>
>> --
>> M.Sc. Andreas Tosstorff
>> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie Department
>> Pharmazie LMU München Butenandtstr. 5-13 ( Haus B)
>> 81377 München
>> Germany
>> Tel.: +49 89 2180 77059
>>
>>
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> --
> M.Sc. Andreas Tosstorff
> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie Department
Pharmazie LMU München Butenandtstr. 5-13 ( Haus B)
> 81377 München
> Germany
> Tel.: +49 89 2180 77059
>
>
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> _______________________________________________
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--
M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Germany
Tel.: +49 89 2180 77059
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Mar 27 2017 - 08:30:03 PDT
